mapping_file	subject_level	subject_code	curation_status	mapping_scope	target_go_id	target_go_label	target_aspect	flags	scrutiny_decision	rationale
autophagy_lysosome_pathway.yaml	class	Autophagy-Lysosome Pathway|Autophagic lysosome reformation	context_only	too_broad_to_propagate	GO:0007040	lysosome organization		high_level_source;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	Autophagic lysosome reformation is the lysosome-regeneration phase that follows autolysosome formation and cargo degradation. As a class, it is better aligned to lysosome organization than to generic autophagy, but the PN members are mechanistically mixed across membrane remodeling, tubulation, product efflux, and unknown late-stage roles, so class-level propagation would still over-annotate.
autophagy_lysosome_pathway.yaml	class	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation	context_only	too_broad_to_propagate	GO:0016236	macroautophagy		high_level_source;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This class is a real macroautophagy context, but its descendants include core factors, component buckets, upstream modulators, localization roles, and residual categories. Projecting generic macroautophagy from this ancestor creates TRAPP-like overpropagation, so candidate GO annotations must come from narrower curated nodes.
autophagy_lysosome_pathway.yaml	class	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion	context_only	too_broad_to_propagate	GO:0016236	macroautophagy		high_level_source;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This class is a late macroautophagy context, but the subtree mixes docking, fusion, localization, membrane-composition, and unknown late-stage roles. The class-level relation is useful for display while propagation is restricted to narrower mechanism nodes.
autophagy_lysosome_pathway.yaml	class	Autophagy-Lysosome Pathway|Autophagy gene expression	context_only	too_broad_to_propagate	GO:0010506	regulation of autophagy		high_level_source;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This class records autophagy-linked gene-expression programs, but many nodes are transcription program names or upstream modulators rather than direct GO regulation assertions. It is kept as context only; transcription factor or cofactor activities are mapped at narrower nodes.
autophagy_lysosome_pathway.yaml	class	Autophagy-Lysosome Pathway|Chaperone-mediated autophagy	context_only	too_broad_to_propagate	GO:0061684	chaperone-mediated autophagy		high_level_source;too_broad_to_propagate	context_only_not_projected	The class label matches the GO CMA process, but the subtree includes both effectors and positive or negative modulators. The relation is retained as context so modulators are not projected as direct CMA participants unless a narrower node supports it.
autophagy_lysosome_pathway.yaml	class	Autophagy-Lysosome Pathway|Microautophagy	context_only	too_broad_to_propagate	GO:0016237	microautophagy		high_level_source;too_broad_to_propagate	context_only_not_projected	The class names a real GO process, but the subtree includes machinery components and mitochondrion-derived-vesicle contexts as well as process labels. Propagation is restricted to narrower nodes.
autophagy_lysosome_pathway.yaml	class	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling	context_only	too_broad_to_propagate	GO:0010506	regulation of autophagy		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This class organizes upstream signaling inputs to autophagy initiation. Because the subtree contains generic insulin, AMPK, mTORC1, nutrient-sensing, and miscellaneous signaling components, class-level propagation to regulation of autophagy would over-annotate many genes.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagic lysosome reformation|Efflux of autophagy products	mapped	ok_for_propagation_to_go	GO:0007041	lysosomal transport		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN leaf denotes export of degradation products from the autolysosome during late-stage autophagic lysosome reformation. The closest current GO process term is lysosomal transport, because the key shared semantics are transport across the lysosomal/autolysosomal membrane rather than a specific cargo chemistry.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagic lysosome reformation|Lysosomal tubulation	context_only	too_broad_to_propagate	GO:0007040	lysosome organization		high_level_source;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN group specifically captures the tubulation and membrane-remodeling step that regenerates lysosomes from autolysosomes. That aligns better to lysosome organization than to generic autophagy, but the current member set mixes factors annotated in GO to lysosome localization and phagosome/lysosome fusion rather than a clean shared lysosome-organization process role, so propagation would overstate the evidence.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		high_level_source;source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		high_level_source;source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-endosome docking	context_only	too_broad_to_propagate	GO:0061910	autophagosome-endosome fusion		high_level_source;too_broad_to_propagate	context_only_not_projected	Reviewed as an autophagosome-endosome docking context. The descendants currently resolve to machinery such as SNARE components, so the broad fusion relation is retained for context but not propagated.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		high_level_source;too_broad_to_propagate	context_only_not_projected	Reviewed as an autophagosome-lysosome docking context. The subtree mixes component buckets and modulators, so generic fusion propagation should come only from narrower reviewed mechanism leaves.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Ca2+ efflux	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		high_level_source;too_broad_to_propagate	context_only_not_projected	Reviewed as a calcium-efflux context in late autophagosome handling. The label supports relation to fusion biology but not universal propagation to the fusion process.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Class 3 PI3K complex 2, direct	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		high_level_source;source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Localization of the autophagosome	mapped	ok_for_propagation_to_go	GO:0061906	autophagosome localization		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This group is explicitly about positioning/autophagosome localization in late autophagy. Autophagosome localization is the correct propagation target rather than autophagosome-lysosome fusion.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Localization of the lysosome	mapped	ok_for_propagation_to_go	GO:0032418	lysosome localization		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This group is explicitly about lysosome positioning in late autophagy. Lysosome localization is the correct propagation target rather than autophagosome-lysosome fusion.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Regulation of autophagosome membrane composition	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		high_level_source;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a membrane-composition context for late autophagosome handling. The parent is too mixed for generic fusion propagation; narrower leaves carry the safe assertions.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Sealing of autophagophore membrane	mapped	ok_for_propagation_to_go	GO:0000045	autophagosome assembly		high_level_source	manual_gene_level_review_required_before_gene_review_change	This group captures autophagophore closure/sealing, a late step in autophagosome assembly. Autophagosome assembly is the safer process target than autophagosome-lysosome fusion.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagy gene expression|Transcriptional coactivator	mapped	ok_for_propagation_to_go	GO:0003713	transcription coactivator activity		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group contains YAP/TAZ coactivator members assigned to autophagy-linked gene-expression control. The shared GO assertion is transcription coactivator activity.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Autophagy gene expression|Transcriptional repressor	mapped	ok_for_propagation_to_go	GO:0003714	transcription corepressor activity		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group is explicitly curated as transcriptional repressors in autophagy-linked expression programs. The safe shared GO target is transcription corepressor activity.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Chaperone-mediated autophagy|Effectors of chaperone-mediated autophagy	mapped	ok_for_propagation_to_go	GO:0061684	chaperone-mediated autophagy		high_level_source	manual_gene_level_review_required_before_gene_review_change	This group covers direct CMA machinery and substrate-selection effectors, unlike the broader CMA class that also includes regulators. Propagation to chaperone-mediated autophagy is appropriate at this narrower level.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Lysosomal catabolism|Lysosomal carbohydrate catabolism	context_only	too_broad_to_propagate	GO:0016052	carbohydrate catabolic process		high_level_source;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This group is a carbohydrate-catabolism context, but the subtree contains multiple enzyme classes and helper roles. Specific molecular functions are mapped at the type level.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Lysosomal catabolism|Lysosomal lipid catabolism	context_only	too_broad_to_propagate	GO:0016042	lipid catabolic process		high_level_source;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This group is a lysosomal lipid-catabolism context, but it mixes lipases, phospholipases, sphingolipid enzymes, and activators. Specific molecular functions are mapped at narrower leaves.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Lysosomal catabolism|Lysosomal nuclease	mapped	ok_for_propagation_to_go	GO:0004518	nuclease activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This group is restricted to lysosomal DNASE2-family nucleases, so nuclease activity is a safe shared molecular-function target.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Lysosomal catabolism|Lysosomal phosphatase	mapped	ok_for_propagation_to_go	GO:0016791	phosphatase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This group contains lysosomal acid-phosphatase members, so phosphatase activity is the shared molecular-function target.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Lysosomal catabolism|Lysosomal protein catabolism	context_only	too_broad_to_propagate	GO:1905146	lysosomal protein catabolic process		high_level_source;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This group is a lysosomal protein-catabolism context, but it includes peptidases plus processing and redox roles. Specific molecular functions are mapped at the type level.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Lysosomal catabolism|Lysosomal sulfatase	mapped	ok_for_propagation_to_go	GO:0008484	sulfuric ester hydrolase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This group contains multiple lysosomal sulfatases with different substrates. The broad sulfuric ester hydrolase activity term captures the shared chemistry without over-specifying one substrate.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Microautophagy|Endosomal microautophagy	mapped	ok_for_propagation_to_go	GO:0061738	late endosomal microautophagy		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group contains HSPA8/co-chaperone machinery for endosomal microautophagy. The matching GO process is late endosomal microautophagy.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Microautophagy|Micromitophagy	context_only	too_broad_to_propagate	GO:0000424	micromitophagy		high_level_source;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	The group is a micromitophagy context, but the descendants are mitochondrion-derived-vesicle budding, docking, HOPS, SNARE, and ubiquitination roles. Direct propagation should come from narrower component or mechanism leaves.
autophagy_lysosome_pathway.yaml	group	Autophagy-Lysosome Pathway|Microautophagy|Microreticulophagy	context_only	too_broad_to_propagate	GO:0061709	reticulophagy		high_level_source;too_broad_to_propagate	context_only_not_projected	This group is an ER-autophagy context, but the source label is microreticulophagy and the members mix core autophagy factors with SEC62. Reticulophagy is kept as context only pending a more specific GO term or gene-level review.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ATG8 homolog processing, direct|Deubiquitination of ATG8 homologs	mapped	ok_for_propagation_to_go	GO:0016579	protein deubiquitination		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes deubiquitination of ATG8-family proteins within the autophagy pathway. GO does not currently provide an ATG8-specific deubiquitination term, so the defensible target is the broader parent process protein deubiquitination.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Autophagy component recruitment to autophagophore|TRAPP complex component	mapped	ok_for_propagation_to_go	GO:0030008	TRAPP complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf is a curated component bucket for TRAPP subunits used in autophagophore recruitment. The matching GO cellular-component term is TRAPP complex, and the member genes already converge strongly on that assignment in existing GOA.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Class 3 PI3K complex 1 component	mapped	ok_for_propagation_to_go	GO:0034271	phosphatidylinositol 3-kinase complex, class III, type I		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type is a curated component class for the direct autophagy- promoting class III PI3K complex 1. Propagation to the matching GO cellular-component term is appropriate, although the source is a component-role category rather than the complex term itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Inflammation related autophagy regulation	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Localization of class 3 PI3K complex 1	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 activity	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 assembly	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|Class 3 PI3K complex 1 signal integration	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|ER stress signaling pathway	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|Hypoxia signaling pathway	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|Insulin signaling pathway	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|MAPK8 signaling pathway	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|Modulator of class 3 PI3K complex 1 activity	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|ATG16L1-positive plasma membrane input	mapped	ok_for_propagation_to_go	GO:1905686	positive regulation of plasma membrane repair		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type captures the ATG16L1-linked plasma-membrane input to the autophagophore membrane pool. The source label is still centered on a membrane-repair / membrane-input mechanism, so propagation to positive regulation of plasma membrane repair is the safest supported GO target.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|ATG2-WIPI complex component	mapped	ok_for_propagation_to_go	GO:0062079	ATG2-ATG18 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN component bucket corresponds to the ATG2-WIPI/ATG18 lipid-transfer complex used during autophagophore membrane expansion. The GO ATG2-ATG18 complex term is the closest component-level target.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|ATG9 homolog	mapped	ok_for_propagation_to_go	GO:0017128	phospholipid scramblase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf is restricted to the ATG9-family proteins, and both human members already support phospholipid scramblase activity in GOA. That MF is the clearest shared mechanistic target exposed by the current ontology.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|ATG9 localization	context_only	too_broad_to_propagate	GO:0034497	protein localization to phagophore assembly site		source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN leaf groups factors that help position ATG9 in the phagophore-initiation system. The closest available GO process term is protein localization to phagophore assembly site, but the current member set mixes direct trafficking regulators with broader upstream factors.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|PI(3)P sequestration	mapped	ok_for_propagation_to_go	GO:0032266	phosphatidylinositol-3-phosphate binding		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf denotes sequestration of PI(3)P at the nascent autophagophore membrane. The current single-gene member, ZFYVE1, already supports phosphatidylinositol-3-phosphate binding, which is the clearest shared GO function exposed by the ontology.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|PI(4)P production	mapped	ok_for_propagation_to_go	GO:0004430	1-phosphatidylinositol 4-kinase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf denotes production of PI(4)P as a membrane-composition input to autophagophore formation. The member gene PI4KB already supports the matching catalytic GO molecular function 1-phosphatidylinositol 4-kinase activity.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|Regulates cholesterol transfer to autophagophore	mapped	ok_for_propagation_to_go	GO:0120020	cholesterol transfer activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type is explicitly about cholesterol transfer into the autophagophore membrane system. The GO cholesterol transfer activity term preserves the core mechanism without overcommitting to a broader autophagy process term.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|Regulation of PI(3)P levels	mapped	ok_for_propagation_to_go	GO:0046856	phosphatidylinositol dephosphorylation		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf groups MTMR-family factors that reduce PI(3)P levels during autophagophore membrane regulation. The strongest shared GO process signal across the member genes is phosphatidylinositol dephosphorylation.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ULK1 pathway, direct|Localization of ULK1 complex	context_only	too_broad_to_propagate	GO:0034497	protein localization to phagophore assembly site		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN leaf groups factors that position the ULK1 initiation complex at the nascent phagophore system. The closest current GO term is protein localization to phagophore assembly site, but the leaf mixes direct tethering or trafficking factors with broader membrane-contact and transport biology.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ULK1 pathway, direct|ULK1 complex component	mapped	ok_for_propagation_to_go	GO:1990316	Atg1/ULK1 kinase complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN leaf is a direct component class for the ULK1 initiation complex. The matching GO cellular-component term is Atg1/ULK1 kinase complex, and the core members already support that assignment in GOA.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-endosome docking|Lysosome-endosome SNARE complex	mapped	ok_for_propagation_to_go	GO:0031201	SNARE complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This leaf is a SNARE machinery bucket in the autophagosome-endosome docking context. The shared gene-level assertion is SNARE complex membership.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|ATG8-LAMP1 interaction modulator	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a docking-interface modulator. It is relevant to autophagosome-lysosome fusion but should not project the full fusion process to all members without gene-level review.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|ATG8-LAMP2 interaction modulator	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a docking-interface modulator. It is relevant to autophagosome-lysosome fusion but should not project the full fusion process to all members without gene-level review.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|BORC complex component	mapped	ok_for_propagation_to_go	GO:0099078	BORC complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This leaf is restricted to BORC complex components, so the BORC complex cellular-component term is the direct propagation target.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|HOPS complex component	mapped	ok_for_propagation_to_go	GO:0030897	HOPS complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type groups genes that are components of the HOPS tethering complex in the autophagosome-lysosome docking step. That supports propagation to the GO cellular-component term for HOPS complex.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|HOPS-BORC interaction mediator	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		too_broad_to_propagate	context_only_not_projected	Reviewed as an interaction-mediator bucket in autophagosome-lysosome docking. The relation to fusion is contextual and should not project generic fusion to all members.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|Lysosome-autophagosome SNARE complex	mapped	ok_for_propagation_to_go	GO:0031201	SNARE complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This leaf is restricted to SNARE machinery for lysosome-autophagosome docking. The shared GO assertion is SNARE complex membership.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|Lysosome-autophagosome interaction modulator	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a modulator bucket for the lysosome-autophagosome interface. The relation to fusion is contextual and too broad for direct propagation.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|Recruitment of HOPS complex to autophagosome	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a HOPS-recruitment context. Specific child leaves map to autophagosome maturation; the parent should not project the full fusion process.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|Tethering factor recruitment	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a tethering-factor recruitment context. The label is relevant to fusion but too broad to propagate as the fusion process for all members.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Class 3 PI3K complex 2, direct|Class 3 PI3K complex 2 component	mapped	ok_for_propagation_to_go	GO:0034272	phosphatidylinositol 3-kinase complex, class III, type II		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type denotes component membership in the direct class III PI3K complex 2 module used during autophagosome maturation and lysosome fusion. The corresponding GO complex term is the right propagation target.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Class 3 PI3K complex 2, direct|Modulator of class 3 PI3K complex 2 activity	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Localization of the autophagosome|Movement of autophagosomes along actin	mapped	ok_for_propagation_to_go	GO:0061906	autophagosome localization		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This leaf describes a mechanism for positioning autophagosomes. The safe shared GO target is autophagosome localization, not the downstream fusion process.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Localization of the autophagosome|Movement of autophagosomes along microtubules	mapped	ok_for_propagation_to_go	GO:0061906	autophagosome localization		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This leaf describes a mechanism for positioning autophagosomes. The safe shared GO target is autophagosome localization, not the downstream fusion process.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Localization of the autophagosome|Recruitment of autophagosome to vicinity of ER	mapped	ok_for_propagation_to_go	GO:0061906	autophagosome localization		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This leaf describes a mechanism for positioning autophagosomes. The safe shared GO target is autophagosome localization, not the downstream fusion process.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Localization of the autophagosome|Retrograde transport along axons	mapped	ok_for_propagation_to_go	GO:0061906	autophagosome localization		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This leaf describes a mechanism for positioning autophagosomes. The safe shared GO target is autophagosome localization, not the downstream fusion process.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Regulation of autophagosome membrane composition|ATG8 homolog de-lipidation	context_only	too_broad_to_propagate	GO:0051697	protein delipidation		source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as an ATG8 delipidation context. The child leaf maps to protein delipidation directly, so the parent is retained as context only.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Regulation of autophagosome membrane composition|PIKFYVE complex component	context_only	too_broad_to_propagate	GO:0061909	autophagosome-lysosome fusion		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a PIKFYVE-complex context in late autophagosome membrane regulation. The local GO cache does not expose a PIKFYVE complex term, so no component propagation is made.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Sealing of autophagophore membrane|ESCRT-I complex component	mapped	ok_for_propagation_to_go	GO:0000813	ESCRT I complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This leaf is restricted to ESCRT-I components used in autophagophore sealing. The shared GO assertion is ESCRT I complex membership.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Sealing of autophagophore membrane|ESCRT-III complex activity modulator	context_only	too_broad_to_propagate	GO:0000815	ESCRT III complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as an ESCRT-III activity modulator. It is related to ESCRT-III but should not project ESCRT-III complex membership to all members.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Sealing of autophagophore membrane|ESCRT-III complex component	mapped	ok_for_propagation_to_go	GO:0000815	ESCRT III complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type is a structural component class for ESCRT-III factors used in autophagophore sealing. The matching GO cellular-component term is ESCRT III complex, which is more precise than the broader late-fusion process mapping.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|AP-1 transcriptional program|Component of AP-1 transcription factor	mapped	ok_for_propagation_to_go	GO:0035976	transcription factor AP-1 complex		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is a component bucket for FOS/JUN-family AP-1 members. The GO transcription factor AP-1 complex term captures the shared component-level assertion.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|ATF4 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|ATF5 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|ATF6/CEBPB transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|DDIT3 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|E2F1 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|FOXO transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|GATA1 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|GATA4 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|HIF1A transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|IRF8 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|NFE2L2 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|NFkB transcriptional program|Component of NFkB transcription factor	mapped	ok_for_propagation_to_go	GO:0071159	NF-kappaB complex		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is restricted to NF-kappaB transcription-factor subunits. The matching GO cellular-component term is NF-kappaB complex.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|SOX2 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|SREBF2 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|STAT3 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|STAT6 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|TCF7L2 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|TFE3 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|TFEB transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|TP53 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|TP63 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|TP73 transcriptional program|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is explicitly restricted to transcription-factor members of an autophagy-linked expression program. The safe shared GO assertion is DNA-binding transcription factor activity, not regulation of autophagy itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy gene expression|Transcriptional coactivator|Cellular mechanics sensing	mapped	ok_for_propagation_to_go	GO:0003713	transcription coactivator activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf contains YAP/TAZ cellular-mechanics sensors whose shared gene-level role is transcription coactivator activity. The autophagy-program context should not be converted into regulation of autophagy for every member.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Autophagosome formation for selective autophagy|Mitophagy	mapped	ok_for_propagation_to_go	GO:0000423	mitophagy		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes the autophagosome-formation machinery used specifically for mitophagy. The source is a mechanistic substep within the broader mitophagy process, so propagation rather than strict equivalence is appropriate.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Autophagy receptor regulation|Mitophagy	mapped	ok_for_propagation_to_go	GO:0000423	mitophagy		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The PN receptor-regulation type for mitophagy captures factors that tune receptor activity within the mitophagy pathway. This supports propagation to mitophagy while preserving that the source is a regulatory sub-role.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Autophagy receptor regulation|Xenophagy	mapped	ok_for_propagation_to_go	GO:0098792	xenophagy		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type groups receptor-regulatory factors assigned to xenophagy. The source category sits inside the xenophagy mechanism rather than being equivalent to the full process.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Marking substrates for selective autophagy|Mitophagy	mapped	ok_for_propagation_to_go	GO:0000423	mitophagy		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The PN marking category for mitophagy captures upstream cargo-marking steps that commit mitochondrial substrates to the mitophagy pathway. That supports propagation to mitophagy.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Aggrephagy	mapped	ok_for_propagation_to_go	GO:0035973	aggrephagy		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN path denotes receptors that recognize aggregation cargo for the aggrephagy pathway. The category is not identical to the GO process term, but propagation to aggrephagy is appropriate because membership in this receptor class implies direct participation in that process.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|ERphagy	mapped	ok_for_propagation_to_go	GO:0061709	reticulophagy		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	The PN uses the community label ERphagy for selective autophagy of the endoplasmic reticulum, while GO uses the synonym reticulophagy. Receptor members of this PN category are suitable for propagation to the GO reticulophagy process.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Ferritinophagy	mapped	ok_for_propagation_to_go	GO:0160247	autophagy cargo adaptor activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	The PN ferritinophagy receptor category captures factors such as NCOA4 that bind ferritin cargo and recruit the autophagy machinery. GO does not currently provide a dedicated ferritinophagy process term in the local ontology cache, so autophagy cargo adaptor activity is the narrowest defensible target.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Glycophagy	mapped	ok_for_propagation_to_go	GO:0061723	glycophagy		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN path groups receptors dedicated to selective glycogen autophagy. The receptor role is narrower than the full pathway, but members of this class can reasonably propagate to the GO glycophagy process.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Individual substrates	mapped	ok_for_propagation_to_go	GO:0160247	autophagy cargo adaptor activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN category groups receptors such as TRIM-family factors that bind specific substrates and recruit autophagy components for their turnover. That aligns best with autophagy cargo adaptor activity rather than with a single selective-autophagy process term.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Lysophagy	mapped	ok_for_propagation_to_go	GO:0160247	autophagy cargo adaptor activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	The PN lysophagy receptor class denotes factors that recognize damaged lysosomal cargo and couple it to autophagic clearance. Since the current GO cache lacks a dedicated lysophagy process term, autophagy cargo adaptor activity is the most specific supported target.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Midbody autophagy	mapped	ok_for_propagation_to_go	GO:0160247	autophagy cargo adaptor activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	Midbody-autophagy receptors such as SQSTM1 link ubiquitinated midbody material to the autophagy machinery. GO does not currently expose a dedicated midbody-autophagy process term in the local ontology cache, so the receptor activity term is the best available mapping target.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Mitophagy	mapped	ok_for_propagation_to_go	GO:0000423	mitophagy		source_contains_domain_or_family_metadata;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN path denotes selective-autophagy receptors for mitochondrial cargo. The source category is a mechanistic sub-role within mitophagy, so propagation rather than exact equivalence is the correct scope.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Nucleophagy	mapped	ok_for_propagation_to_go	GO:0044804	nucleophagy		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	Receptors in this PN category participate specifically in selective autophagic turnover of nuclear material. That supports propagation to the GO nucleophagy process even though the PN source is receptor-centric.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Pexophagy	mapped	ok_for_propagation_to_go	GO:0000425	pexophagy		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN path groups receptors for selective autophagic turnover of peroxisomes. The role is part of, but not equivalent to, the full GO pexophagy process, so propagation scope is appropriate.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Ribophagy	mapped	ok_for_propagation_to_go	GO:0034517	ribophagy		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	The PN category covers receptors for autophagic turnover of ribosomes. These genes belong in the ribophagy process, but the PN label denotes a receptor role rather than the entire process class.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Synaptophagy	mapped	ok_for_propagation_to_go	GO:0160247	autophagy cargo adaptor activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	The PN synaptophagy receptor category includes factors that recruit synaptic cargo to autophagosomes. Because the validated GO cache has no dedicated synaptophagy process term, autophagy cargo adaptor activity is the narrowest current target that preserves the receptor semantics.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Xenophagy	mapped	ok_for_propagation_to_go	GO:0098792	xenophagy		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN category captures receptors for selective autophagy of pathogens or pathogen-derived material. The receptor class is narrower than the GO xenophagy process, so this is a propagation mapping.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Substrate selectivity regulator for selective autophagy|Aggrephagy	mapped	ok_for_propagation_to_go	GO:0035973	aggrephagy		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	The PN substrate-selectivity-regulator type for aggrephagy captures factors that determine cargo choice within the aggrephagy pathway. The source label is a regulator sub-role, so propagation is appropriate.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Substrate selectivity regulator for selective autophagy|Lysophagy	mapped	ok_for_propagation_to_go	GO:0160247	autophagy cargo adaptor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes lysophagy selectivity regulators. Because the local GO cache does not expose a dedicated lysophagy term, autophagy cargo adaptor activity is the best supported propagation target.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Substrate selectivity regulator for selective autophagy|Mitophagy	mapped	ok_for_propagation_to_go	GO:0000423	mitophagy		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type groups substrate-selectivity regulators assigned to mitophagy. Those factors participate in mitophagy, but the PN category is more specific than the full process term.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Autophagy substrate selection|Substrate selectivity regulator for selective autophagy|Pexophagy	mapped	ok_for_propagation_to_go	GO:0000425	pexophagy		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes selectivity regulators that direct substrates into the pexophagy pathway. Propagation to pexophagy is justified, but the source label is narrower than the process itself.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Chaperone-mediated autophagy|Effectors of chaperone-mediated autophagy|Receptor for chaperone-mediated autophagy	mapped	ok_for_propagation_to_go	GO:0061684	chaperone-mediated autophagy		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This leaf is restricted to the lysosomal CMA receptor role, so the CMA process term is a supported process-level target.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Chaperone-mediated autophagy|Extralysosomal modulator of chaperone-mediated autophagy|Chaperone-mediated autophagy enhancer	mapped	ok_for_propagation_to_go	GO:1904716	positive regulation of chaperone-mediated autophagy		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type explicitly records enhancer roles for CMA. The directional GO regulation term is more accurate than projecting direct participation in CMA from the class ancestor.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Chaperone-mediated autophagy|Extralysosomal modulator of chaperone-mediated autophagy|Chaperone-mediated autophagy inhibitor	mapped	ok_for_propagation_to_go	GO:1904715	negative regulation of chaperone-mediated autophagy		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type explicitly records inhibitory roles for CMA. The directional GO regulation term is more accurate than projecting direct participation in CMA from the class ancestor.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Chaperone-mediated autophagy|Lysosomal modulator of chaperone-mediated autophagy|Chaperone-mediated autophagy enhancer	mapped	ok_for_propagation_to_go	GO:1904716	positive regulation of chaperone-mediated autophagy		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type explicitly records enhancer roles for CMA. The directional GO regulation term is more accurate than projecting direct participation in CMA from the class ancestor.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Chaperone-mediated autophagy|Lysosomal modulator of chaperone-mediated autophagy|Chaperone-mediated autophagy inhibitor	mapped	ok_for_propagation_to_go	GO:1904715	negative regulation of chaperone-mediated autophagy		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type explicitly records inhibitory roles for CMA. The directional GO regulation term is more accurate than projecting direct participation in CMA from the class ancestor.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Lysosomal catabolism|Regulation of lysosomal environment|Lysosomal acidification	mapped	ok_for_propagation_to_go	GO:0007042	lysosomal lumen acidification		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group directly names the lysosomal acidification mechanism. Propagation to the GO lysosomal lumen acidification term is an exact mechanistic match.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Microautophagy|General microautophagy machinery|ESCRT-III complex component	mapped	ok_for_propagation_to_go	GO:0000815	ESCRT III complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This leaf is a component bucket for ESCRT-III machinery used in microautophagy contexts. The shared GO assertion is ESCRT III complex membership.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|AMPK signaling pathway, direct|AMPK complex component	mapped	ok_for_propagation_to_go	GO:0031588	nucleotide-activated protein kinase complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is restricted to AMPK alpha, beta, and gamma subunits. The local GO cache uses nucleotide-activated protein kinase complex for this component-level assertion.
autophagy_lysosome_pathway.yaml	type	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, direct|mTORC1 complex component	mapped	ok_for_propagation_to_go	GO:0031931	TORC1 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf is a component bucket for mTORC1/TORC1 machinery. The matching GO cellular-component target is TORC1 complex.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ATG8 homolog processing, direct|Preparation of ATG8 homologs for lipidation|ATG8 homolog	mapped	ok_for_propagation_to_go	GO:0061739	protein lipidation involved in autophagosome assembly		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf denotes the ATG8-family proteins that are the direct substrates of the lipidation step during autophagophore growth. The best current GO target is the corresponding process term for protein lipidation in autophagosome assembly.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ATG8 homolog processing, direct|Preparation of ATG8 homologs for lipidation|Component of E3-like ATG5-ATG12-ATG16 complex that transfers ATG8 to PE	mapped	ok_for_propagation_to_go	GO:0034274	Atg12-Atg5-Atg16 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype explicitly denotes a component of the E3-like ATG5-ATG12-ATG16 complex used in ATG8 lipidation. The matching GO cellular-component term for the Atg12-Atg5-Atg16 complex is the correct propagation target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ATG8 homolog processing, direct|Preparation of ATG8 homologs for lipidation|E2-like enzyme conjugated to ATG8 before transfer to PE	mapped	exact	GO:0141046	Atg8-family conjugating enzyme activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf is an enzyme-role class for the E2-like factor that conjugates ATG8-family proteins before transfer to phosphatidylethanol- amine. The matching GO molecular function term is an exact fit.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ATG8 homolog processing, direct|Preparation of ATG8 homologs for lipidation|Protease that removes C-terminal Arg from ATG8	mapped	ok_for_propagation_to_go	GO:0008234	cysteine-type peptidase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is restricted to ATG4-family proteases that process ATG8-family proteins before lipidation. GO lacks an ATG4-specific activity in the local cache, so cysteine-type peptidase activity is the safest shared molecular-function target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ATG8 homolog processing, upstream|Preparation of ATG8 homologs for lipidation|Localization of ATG5-ATG12-ATG16 complex	context_only	too_broad_to_propagate	GO:0034497	protein localization to phagophore assembly site		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN subtype captures localization control for the ATG5-ATG12-ATG16 complex during ATG8 lipidation. The closest GO concept is localization to the phagophore assembly site rather than the complex cellular-component term itself.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ATG8 homolog processing, upstream|Preparation of ATG8 homologs for lipidation|Modulation of ATG4 activity	mapped	ok_for_propagation_to_go	GO:2000785	regulation of autophagosome assembly		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN leaf denotes factors that alter ATG4 function upstream of ATG8 processing. The cleanest GO-level consequence captured in the current ontology is regulation of autophagosome assembly.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|ATG8 homolog processing, upstream|Preparation of ATG8 homologs for lipidation|Processing of ATG5-ATG12-ATG16 complex components	mapped	ok_for_propagation_to_go	GO:0032446	protein modification by small protein conjugation		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf groups the upstream processing/conjugation machinery that modifies components feeding into the ATG5-ATG12-ATG16 module. The strongest shared GO process target is protein modification by small protein conjugation.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 activity|Modulator of ATG14L	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 activity|Modulator of BECN1 availability	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 activity|Modulator of BECN1 localization	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 activity|Modulator of BECN1 phosphorylation	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 activity|Modulator of BECN1 ubiquitination	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 activity|Modulator of PIK3C3/VPS34 NEDDylation	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 activity|Modulator of PIK3C3/VPS34 activity	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 activity|Modulator of PIK3C3/VPS34 ubiquitination	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 assembly|Exocyst complex assembly modulator	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, direct|Modulator of class 3 PI3K complex 1 assembly|Recruits PI3K complex 1 components to exocyst complex	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|Class 3 PI3K complex 1 signal integration|Modulator of BECN1 availability via DAPK	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|ER stress signaling pathway|Modulator of BECN1 availability	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|Hypoxia signaling pathway|Modulator of BECN1 availability	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|Insulin signaling pathway|Modulator of BECN1 availability	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Class 3 PI3K complex 1, upstream|MAPK8 signaling pathway|Modulator of BECN1 availability	context_only	too_broad_to_propagate	GO:0035032	phosphatidylinositol 3-kinase complex, class III		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	Reviewed as a class-III PI3K complex context or regulator bucket. This node is useful for curator interpretation, but it should not project cellular-component membership; only explicit complex-component leaves propagate to GO complex terms.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|ATG16L1-positive plasma membrane input|Autophagophore-vesicle SNARE complex	mapped	ok_for_propagation_to_go	GO:1905686	positive regulation of plasma membrane repair		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN subtype is a more specific ATG16L1-positive membrane-input node nested under the same membrane-repair mechanism. Propagation to the same GO target remains biologically centered and conservative.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|ATG16L1-positive plasma membrane input|Autophagophore-vesicle SNARE complex regulator	mapped	ok_for_propagation_to_go	GO:1905686	positive regulation of plasma membrane repair		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes a regulatory role in the same ATG16L1-linked plasma-membrane input mechanism. The membrane-repair GO term is still the cleanest propagation target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagophore initiation and elongation|Regulation of autophagophore membrane composition|ER membrane input|COPII vesicle component	mapped	ok_for_propagation_to_go	GO:0030127	COPII vesicle coat		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf groups the core COPII coat machinery that contributes ER membrane input to autophagophore formation. The strongest shared GO cellular-component signal across the member genes is COPII vesicle coat.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|Recruitment of HOPS complex to autophagosome|ATG8 homolog	mapped	ok_for_propagation_to_go	GO:0097352	autophagosome maturation		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf captures ATG8-family proteins in their specific role of recruiting HOPS machinery during late autophagosome handling. The best GO process target for that shared role is autophagosome maturation.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|Recruitment of HOPS complex to autophagosome|Bridges ATG8 and HOPS complex	mapped	ok_for_propagation_to_go	GO:0097352	autophagosome maturation		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf denotes a direct bridging factor that links ATG8 proteins to HOPS recruitment on late autophagic membranes. That is a narrow mechanistic role within autophagosome maturation.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Autophagosome-lysosome docking|Recruitment of HOPS complex to autophagosome|Bridges STX17, RUBCNL and HOPS complex	mapped	ok_for_propagation_to_go	GO:0097352	autophagosome maturation		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf captures a direct bridging factor that couples autophagosome SNARE and HOPS-recruitment machinery during the late fusion-ready stage. The corresponding GO process is autophagosome maturation.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Localization of the autophagosome|Movement of autophagosomes along microtubules|ATG8 homolog	mapped	ok_for_propagation_to_go	GO:0061906	autophagosome localization		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN subtype specifically places ATG8-family proteins in the microtubule-dependent positioning of autophagosomes. The cleanest current GO process target is autophagosome localization.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Localization of the autophagosome|Movement of autophagosomes along microtubules|HOPS-BORC complex bridging	mapped	ok_for_propagation_to_go	GO:0061906	autophagosome localization		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes the bridging machinery that links HOPS/BORC-like late-endolysosomal transport systems to autophagosome positioning on microtubules. The best current GO target is autophagosome localization.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Localization of the autophagosome|Movement of autophagosomes along microtubules|Recruitment of dynein-dynactin motor complex	mapped	ok_for_propagation_to_go	GO:0061906	autophagosome localization		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN subtype captures recruitment of dynein-dynactin machinery for autophagosome movement. The mechanistically closest GO process target is autophagosome localization.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagosome closure maturation and lysosome fusion|Regulation of autophagosome membrane composition|ATG8 homolog de-lipidation|Releases ATG8 homologs from maturing autophagosome	mapped	ok_for_propagation_to_go	GO:0051697	protein delipidation		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype specifically denotes removal of lipidated ATG8-family proteins from the maturing autophagosome membrane. The best current GO process target is protein delipidation.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagy substrate selection|Marking substrates for selective autophagy|Lysophagy|ELDR complex component	mapped	ok_for_propagation_to_go	GO:0160247	autophagy cargo adaptor activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	The PN ELDR-complex subtype sits inside lysophagy cargo-marking machinery. In the current GO cache, autophagy cargo adaptor activity is the narrowest supported target for this lysophagy-specific adaptor role.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|Chaperone assisted selective autophagy|CASA complex component	mapped	ok_for_propagation_to_go	GO:0035973	aggrephagy		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	The PN CASA subtype covers BAG3-HSPB8-HSP70-system machinery that directs damaged or aggregation-prone substrates into selective autophagic clearance. GO lacks a dedicated CASA term in the current cache, and this subtype includes chaperones and cofactors beyond pure cargo adaptors, so aggrephagy is the closest available process target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Autophagy substrate selection|Substrate selectivity regulator for selective autophagy|Lysophagy|ELDR complex component	mapped	ok_for_propagation_to_go	GO:0160247	autophagy cargo adaptor activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes the ELDR-complex adaptor role in lysophagy selectivity control. The current GO cache does not provide a more specific lysophagy target than autophagy cargo adaptor activity.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Lysosomal catabolism|Lysosomal lipid catabolism|Lysosomal sphingomyelin/ceramide metabolism|General activator of glycosphingolipid degradation	mapped	ok_for_propagation_to_go	GO:0030290	sphingolipid activator protein activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf corresponds to saposin/prosaposin-like activation of lysosomal glycosphingolipid degradation; sphingolipid activator protein activity is the shared GO target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Lysosomal catabolism|Regulation of lysosomal environment|Lysosomal acidification|Regulator of the lysosomal v-ATPase proton pump	mapped	ok_for_propagation_to_go	GO:0060590	ATPase regulator activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype is a regulator of the lysosomal V-ATPase proton pump. ATPase regulator activity is the narrowest GO target that preserves the source mechanism without requiring a speculative complex-specific term.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Lysosomal catabolism|Regulation of lysosomal environment|Lysosomal acidification|V0 lysosomal v-ATPase proton pump component	mapped	ok_for_propagation_to_go	GO:0033179	proton-transporting V-type ATPase, V0 domain		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes the V0-sector component of the lysosomal V-type ATPase. The GO V0-domain component term is the appropriate propagation target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Lysosomal catabolism|Regulation of lysosomal environment|Lysosomal acidification|V1 lysosomal v-ATPase proton pump component	mapped	ok_for_propagation_to_go	GO:0033176	proton-transporting V-type ATPase complex		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes the V1-sector component of the lysosomal V-ATPase. In the current GO cache, the broader V-type ATPase complex is the safest validated target for this component role.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Microautophagy|Micromitophagy|PDH-positive MDV-mediated micromitophagy|Formation of SNARE complex to dock MDV to lysosome	mapped	ok_for_propagation_to_go	GO:0031201	SNARE complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This leaf contains SNARE machinery used for docking mitochondrion-derived vesicles to lysosomes. The shared gene-level assertion is SNARE complex membership.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Microautophagy|Micromitophagy|PDH-positive MDV-mediated micromitophagy|HOPS complex component	mapped	ok_for_propagation_to_go	GO:0030897	HOPS complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This leaf is restricted to HOPS complex components in a micromitophagy context. The shared GO assertion is HOPS complex membership.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|AMPK signaling pathway, direct|AMPK complex modulator by phosphorylation|AMPK kinase (not in a complex)	mapped	ok_for_propagation_to_go	GO:0004674	protein serine/threonine kinase activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf contains upstream kinases that phosphorylate AMPK. The defensible shared GO assertion is protein serine/threonine kinase activity, not direct regulation of autophagy.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|AMPK signaling pathway, direct|AMPK complex modulator by phosphorylation|IKK complex component	mapped	ok_for_propagation_to_go	GO:0008385	IkappaB kinase complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf groups IKK-complex components in an AMPK/autophagy-signaling context. The shared GO assertion is IkappaB kinase complex membership.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|AMPK signaling pathway, direct|AMPK complex modulator by phosphorylation|PKA complex component	mapped	ok_for_propagation_to_go	GO:0005952	cAMP-dependent protein kinase complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf groups PKA catalytic and regulatory subunits. The shared GO assertion is cAMP-dependent protein kinase complex membership.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Insulin signaling pathway|AKT1 activator, mTORC2 complex component	mapped	ok_for_propagation_to_go	GO:0031932	TORC2 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf contains mTORC2 components in the insulin-to-mTORC1 upstream arm. The shared GO assertion is TORC2 complex membership.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Insulin signaling pathway|PI3K complex component	mapped	ok_for_propagation_to_go	GO:0005943	phosphatidylinositol 3-kinase complex, class IA		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf contains class IA PI3K catalytic/regulatory subunits in the insulin-signaling arm. The matching GO component term is phosphatidylinositol 3-kinase complex, class IA.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Insulin signaling pathway|PIP3 dephosphorylation	mapped	ok_for_propagation_to_go	GO:0016314	phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf is currently PTEN-like PIP3 dephosphorylation upstream of mTORC1; the matching GO molecular function is phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|GATOR1 complex component	mapped	ok_for_propagation_to_go	GO:1990130	GATOR1 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes component membership in the GATOR1 nutrient- sensing complex upstream of mTORC1 and autophagy control. Propagation to the GO cellular-component term for GATOR1 complex is appropriate.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|GATOR1 complex modulator	mapped	ok_for_propagation_to_go	GO:1990130	GATOR1 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype is a GATOR1 complex modulator in the nutrient-sensing arm of mTORC1 control. Propagation to the GO GATOR1 complex term keeps the same nutrient-sensing mechanism.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|GATOR2 complex component	mapped	ok_for_propagation_to_go	GO:0061700	GATOR2 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes component membership in the GATOR2 nutrient- sensing complex upstream of mTORC1 regulation. The matching GO cellular-component term is an appropriate propagation target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|GATOR2 complex modulator	mapped	ok_for_propagation_to_go	GO:0061700	GATOR2 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype is a GATOR2 complex modulator in the same upstream nutrient-sensing module. The GO GATOR2 complex term is the best supported propagation target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|KICSTOR complex component	mapped	ok_for_propagation_to_go	GO:0140007	KICSTOR complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf is a component bucket for the KICSTOR nutrient-sensing complex. The GO KICSTOR complex term is the direct target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|Ragulator complex component	mapped	ok_for_propagation_to_go	GO:0071986	Ragulator complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf is restricted to Ragulator complex subunits. The matching GO cellular-component term is Ragulator complex.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|Regulator of the lysosomal v-ATPase proton pump	mapped	ok_for_propagation_to_go	GO:0060590	ATPase regulator activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN leaf contains ATP6AP-family regulators of the lysosomal V-ATPase. ATPase regulator activity is the safe shared molecular-function target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|V0 lysosomal v-ATPase proton pump component	mapped	ok_for_propagation_to_go	GO:0046610	lysosomal proton-transporting V-type ATPase, V0 domain		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN leaf is restricted to V0-sector lysosomal V-ATPase components. The GO lysosomal V0-domain component term is the direct target.
autophagy_lysosome_pathway.yaml	subtype	Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|V1 lysosomal v-ATPase proton pump component	mapped	ok_for_propagation_to_go	GO:0046612	lysosomal proton-transporting V-type ATPase, V1 domain		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN leaf is restricted to V1-sector lysosomal V-ATPase components. The GO lysosomal V1-domain component term is the direct target.
chaperone_systems.yaml	group	Cytonuclear proteostasis|Folding enzyme|Peptidyl-prolyl isomerases	mapped	ok_for_propagation_to_go	GO:0003755	peptidyl-prolyl cis-trans isomerase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group is the cytonuclear peptidyl-prolyl isomerase branch. The matching GO molecular-function term is appropriate for propagation.
chaperone_systems.yaml	type	Cytonuclear proteostasis|Chaperone|CCT/TRiC system|CCT/TRiC subunit	mapped	ok_for_propagation_to_go	GO:0005832	chaperonin-containing T-complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN path denotes subunits of the cytosolic CCT/TRiC chaperonin complex. Propagation to the GO cellular-component term for the chaperonin-containing T-complex is appropriate, although the PN source is specifically the subunit role class.
chaperone_systems.yaml	type	Cytonuclear proteostasis|Chaperone|HSP70 system|HSP70	mapped	ok_for_propagation_to_go	GO:0140662	ATP-dependent protein folding chaperone		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In the PN hierarchy, the type label HSP70 within the chaperone/HSP70-system context denotes canonical HSP70 chaperones. Propagation to the GO molecular function ATP-dependent protein folding chaperone is appropriate for curation, but the PN family label is not itself a strict GO-equivalent class.
chaperone_systems.yaml	type	Cytonuclear proteostasis|Chaperone|HSP70 system|HSP70 nucleotide exchange inhibitor	mapped	ok_for_propagation_to_go	GO:0030544	Hsp70 protein binding		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type is represented by ST13/HIP, an HSP70 nucleotide-exchange inhibitor. The shared mechanistic assertion is Hsp70 protein binding.
chaperone_systems.yaml	type	Cytonuclear proteostasis|Chaperone|HSP70 system|J-domain containing HSP70 cochaperone	mapped	ok_for_propagation_to_go	GO:0030544	Hsp70 protein binding		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In the PN hierarchy, this type denotes J-domain cochaperones assigned to the HSP70 system. Their shared mechanistic role is direct interaction with HSP70-family chaperones, making Hsp70 protein binding the most defensible GO target in the current cache.
chaperone_systems.yaml	type	Cytonuclear proteostasis|Chaperone|HSP90 system|HSP90	mapped	ok_for_propagation_to_go	GO:0140662	ATP-dependent protein folding chaperone		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In the PN hierarchy, HSP90 within the chaperone/HSP90-system context denotes canonical HSP90 chaperones across multiple proteostasis branches. Propagation to ATP-dependent protein folding chaperone is appropriate, while strict equivalence would overstate the family label as a GO class.
chaperone_systems.yaml	type	Cytonuclear proteostasis|Chaperone|small HSP system|small HSP	mapped	ok_for_propagation_to_go	GO:0044183	protein folding chaperone		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes small heat-shock chaperones. Protein folding chaperone is the appropriate shared molecular-function term.
chaperone_systems.yaml	type	ER proteostasis|Chaperone|HSP70 system|HSP70	mapped	ok_for_propagation_to_go	GO:0140662	ATP-dependent protein folding chaperone		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In the PN hierarchy, the type label HSP70 within the chaperone/HSP70-system context denotes canonical HSP70 chaperones. Propagation to the GO molecular function ATP-dependent protein folding chaperone is appropriate for curation, but the PN family label is not itself a strict GO-equivalent class.
chaperone_systems.yaml	type	ER proteostasis|Chaperone|HSP70 system|J-domain containing HSP70 cochaperone	mapped	ok_for_propagation_to_go	GO:0030544	Hsp70 protein binding		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In the PN hierarchy, this type denotes J-domain cochaperones assigned to the HSP70 system. Their shared mechanistic role is direct interaction with HSP70-family chaperones, making Hsp70 protein binding the most defensible GO target in the current cache.
chaperone_systems.yaml	type	ER proteostasis|Chaperone|HSP90 system|HSP90	mapped	ok_for_propagation_to_go	GO:0140662	ATP-dependent protein folding chaperone		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In the PN hierarchy, HSP90 within the chaperone/HSP90-system context denotes canonical HSP90 chaperones across multiple proteostasis branches. Propagation to ATP-dependent protein folding chaperone is appropriate, while strict equivalence would overstate the family label as a GO class.
chaperone_systems.yaml	type	Mitochondrial proteostasis|Chaperone|HSP70 system|HSP70	mapped	ok_for_propagation_to_go	GO:0140662	ATP-dependent protein folding chaperone		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In the PN hierarchy, the type label HSP70 within the chaperone/HSP70-system context denotes canonical HSP70 chaperones. Propagation to the GO molecular function ATP-dependent protein folding chaperone is appropriate for curation, but the PN family label is not itself a strict GO-equivalent class.
chaperone_systems.yaml	type	Mitochondrial proteostasis|Chaperone|HSP70 system|J-domain containing HSP70 cochaperone	mapped	ok_for_propagation_to_go	GO:0030544	Hsp70 protein binding		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In the PN hierarchy, this type denotes J-domain cochaperones assigned to the HSP70 system. Their shared mechanistic role is direct interaction with HSP70-family chaperones, making Hsp70 protein binding the most defensible GO target in the current cache.
chaperone_systems.yaml	type	Mitochondrial proteostasis|Chaperone|HSP90 system|HSP90	mapped	ok_for_propagation_to_go	GO:0140662	ATP-dependent protein folding chaperone		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In the PN hierarchy, HSP90 within the chaperone/HSP90-system context denotes canonical HSP90 chaperones across multiple proteostasis branches. Propagation to ATP-dependent protein folding chaperone is appropriate, while strict equivalence would overstate the family label as a GO class.
chaperone_systems.yaml	subtype	Cytonuclear proteostasis|Chaperone|HSP70-HSP90 system integration|HSP70-HSP90 joint cochaperone|CC-TPR domain and Ub ligase	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN subtype explicitly denotes TPR-containing ubiquitin ligases in the HSP70/HSP90 co-chaperone branch. The shared catalytic assertion is ubiquitin protein ligase activity.
er_proteostasis.yaml	class	ER proteostasis|Protein transport	mapped	ok_for_propagation_to_go	GO:0015031	protein transport		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The PN ER Protein transport class groups ER-targeting and ER-insertion pathways. GO protein transport is the appropriate propagation target, while the source class remains ER-specific and broader than any single GO transport subtype.
er_proteostasis.yaml	group	ER proteostasis|Folding enzyme|Peptidyl-prolyl isomerases	mapped	ok_for_propagation_to_go	GO:0003755	peptidyl-prolyl cis-trans isomerase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group is the ER peptidyl-prolyl isomerase family. The GO PPIase activity term is the appropriate propagation target for this folding enzyme bucket.
er_proteostasis.yaml	group	ER proteostasis|Folding enzyme|Peroxiredoxins	mapped	ok_for_propagation_to_go	GO:0051920	peroxiredoxin activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group denotes ER peroxiredoxins. The shared molecular function is peroxiredoxin activity.
er_proteostasis.yaml	group	ER proteostasis|Folding enzyme|Protein disulfide isomerases	mapped	ok_for_propagation_to_go	GO:0003756	protein disulfide isomerase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures the canonical ER protein-disulfide-isomerase folding enzymes. GO protein disulfide isomerase activity is the cleanest propagation target for the family bucket.
er_proteostasis.yaml	group	ER proteostasis|Glycoproteostasis|N-glycosylation system	mapped	ok_for_propagation_to_go	GO:0006487	protein N-linked glycosylation		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures the ER N-glycosylation machinery that installs and processes N-linked glycans during proteostasis. GO protein N-linked glycosylation is the best current propagation target in the local cache.
er_proteostasis.yaml	group	ER proteostasis|Glycoproteostasis|O-glycosylation system	mapped	ok_for_propagation_to_go	GO:0006493	protein O-linked glycosylation		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures ER O-glycosylation machinery. Protein O-linked glycosylation is the appropriate shared process target.
er_proteostasis.yaml	group	ER proteostasis|Maturation and folding of specific substrates|ER collagen processing and folding	mapped	ok_for_propagation_to_go	GO:0032964	collagen biosynthetic process		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group contains ER factors dedicated to collagen maturation, processing, and folding. Collagen biosynthetic process captures the shared substrate-specific pathway context.
er_proteostasis.yaml	group	ER proteostasis|Organelle-specific protein degradation|ER associated degradation	mapped	exact	GO:0036503	ERAD pathway		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	"The PN group ""ER associated degradation"" is a direct lexical and biological match to the GO ERAD pathway term. The additional branch and class context disambiguates the source string from any broader degradation language."
er_proteostasis.yaml	group	ER proteostasis|Protein transport|ER signal peptidase	mapped	ok_for_propagation_to_go	GO:0005787	signal peptidase complex		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group denotes ER signal peptidase complex components. The matching GO cellular-component term is the direct propagation target.
er_proteostasis.yaml	group	ER proteostasis|Protein transport|GET pathway component	mapped	ok_for_propagation_to_go	GO:0006620	post-translational protein targeting to endoplasmic reticulum membrane		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The PN GET-pathway group covers machinery for post-translational delivery of tail-anchored membrane proteins to the ER. GO does not model the GET pathway directly in the local cache, and the closest supported process term is post-translational targeting to the ER membrane.
er_proteostasis.yaml	group	ER proteostasis|Protein transport|SEC61 channel complex component	mapped	ok_for_propagation_to_go	GO:0005784	Sec61 translocon complex		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group denotes SEC61 translocon components. The GO Sec61 translocon complex term is the direct cellular-component target.
er_proteostasis.yaml	group	ER proteostasis|Protein transport|SRP receptor subunit	mapped	ok_for_propagation_to_go	GO:0006614	SRP-dependent cotranslational protein targeting to membrane		high_level_source;source_contains_domain_or_family_metadata;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	SRP receptor subunits participate in docking the SRP-ribosome complex to the ER membrane during cotranslational targeting. Mapping to the GO SRP-dependent targeting process is appropriate at propagation scope.
er_proteostasis.yaml	group	ER proteostasis|Protein transport|Signal recognition particle component	mapped	ok_for_propagation_to_go	GO:0006614	SRP-dependent cotranslational protein targeting to membrane		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group captures core signal-recognition-particle machinery used to direct translating ribosome-nascent chain complexes to the ER membrane. The group is machinery-centric rather than process-equivalent, so it propagates to the GO targeting process.
er_proteostasis.yaml	group	ER proteostasis|Protein transport|Transmembrane protein import	mapped	ok_for_propagation_to_go	GO:0044743	protein transmembrane import into intracellular organelle		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group covers ER transmembrane-protein insertion/import systems such as EMC- and PAT-related pathways. The local GO cache does not expose an ER-specific matching term, so the broader intracellular-organelle transmembrane-import process is the best supported propagation target.
er_proteostasis.yaml	type	ER proteostasis|Glycoproteostasis|N-glycosylation system|Oligosaccharyl transferase complex component	mapped	ok_for_propagation_to_go	GO:0008250	oligosaccharyltransferase complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type denotes oligosaccharyltransferase complex components. The GO complex term is the direct cellular-component target.
er_proteostasis.yaml	type	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates	mapped	ok_for_propagation_to_go	GO:0036503	ERAD pathway		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type covers the cytosolic processing steps that receive ERAD substrates after retrotranslocation. These activities remain part of the ERAD pathway, but the source category is a specific mechanistic slice.
er_proteostasis.yaml	type	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|ER handling of ERAD substrates	mapped	ok_for_propagation_to_go	GO:0036503	ERAD pathway		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures ER-lumenal and membrane-local ERAD handling steps prior to retrotranslocation. These steps are mechanistic parts of the broader ERAD pathway, so propagation to ERAD pathway is appropriate.
er_proteostasis.yaml	type	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|VCP system for retrotranslocation in ERAD	mapped	ok_for_propagation_to_go	GO:0036503	ERAD pathway		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures the VCP/p97-dependent retrotranslocation machinery used in ERAD. It is not a separate process from ERAD, but a core mechanistic subsystem within it.
er_proteostasis.yaml	type	ER proteostasis|Protein transport|ER-Golgi trafficking|Anterograde transport	mapped	ok_for_propagation_to_go	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type captures anterograde ER-to-Golgi trafficking factors. The GO ER-to-Golgi vesicle-mediated transport process is the shared target.
er_proteostasis.yaml	type	ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport	mapped	ok_for_propagation_to_go	GO:0006890	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the earlier retrograde-transport bucket has been folded into ER-Golgi trafficking and now specifically denotes COPI/KDEL-style retrograde trafficking from Golgi back to ER. The correct GO target is therefore retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum rather than ER-to-cytosol retrotranslocation.
er_proteostasis.yaml	type	ER proteostasis|Protein transport|Transmembrane protein import|EMC complex component	mapped	ok_for_propagation_to_go	GO:0072546	EMC complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type denotes ER membrane protein complex components. The GO EMC complex cellular-component term is the direct target.
er_proteostasis.yaml	type	ER proteostasis|Protein transport|Transmembrane protein import|PAT complex component	mapped	ok_for_propagation_to_go	GO:0160005	PAT complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type denotes PAT-complex components in ER membrane protein insertion. The GO PAT complex term is the direct target.
er_proteostasis.yaml	subtype	ER proteostasis|Glycoproteostasis|N-glycosylation system|N-glycan processing|Mannose trimming	mapped	ok_for_propagation_to_go	GO:1904382	mannose trimming involved in glycoprotein ERAD pathway		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	Within the ER proteostasis branch, this PN subtype denotes mannose trimming used in glycoprotein quality control and ERAD triage. That is close enough for propagation to the GO mannose-trimming-in-ERAD process, but the PN subtype is framed as a proteostasis step rather than a formal GO process class.
er_proteostasis.yaml	subtype	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|Deglycosylation of ERAD substrates	mapped	ok_for_propagation_to_go	GO:0006517	protein deglycosylation		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes cytosolic deglycosylation of ERAD substrates. Protein deglycosylation is the appropriate shared process target.
er_proteostasis.yaml	subtype	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated DUB	mapped	ok_for_propagation_to_go	GO:0101005	deubiquitinase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes ERAD-associated deubiquitinases. Deubiquitinase activity captures the shared molecular function.
er_proteostasis.yaml	subtype	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated E2 conjugating enzyme	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes ERAD-associated E2 enzymes. Ubiquitin conjugating enzyme activity is the appropriate shared molecular-function target.
er_proteostasis.yaml	subtype	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated RING E3 ligase	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes ERAD-associated RING E3 ligases. Ubiquitin protein ligase activity is the appropriate shared catalytic target.
er_proteostasis.yaml	subtype	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated UBOX E3 ligase	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes ERAD-associated U-box E3 ligases. Ubiquitin protein ligase activity is the appropriate shared catalytic target.
er_proteostasis.yaml	subtype	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated idiosyncratic E3 ligase	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes ERAD-associated E3 ligases with noncanonical architecture. Ubiquitin protein ligase activity is the shared catalytic target.
er_proteostasis.yaml	subtype	ER proteostasis|Organelle-specific protein degradation|ER associated degradation|VCP system for retrotranslocation in ERAD|Intramembrane protease, cleaves unstable membrane proteins, transfers to ERAD	mapped	ok_for_propagation_to_go	GO:0004252	serine-type endopeptidase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype is represented by rhomboid-family intramembrane proteases. Serine-type endopeptidase activity is the shared catalytic target.
er_proteostasis.yaml	subtype	ER proteostasis|Protein transport|ER-Golgi trafficking|Anterograde transport|COPII vesicle component	mapped	ok_for_propagation_to_go	GO:0030127	COPII vesicle coat		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes COPII vesicle coat components. The GO COPII vesicle coat term is the direct complex target.
er_proteostasis.yaml	subtype	ER proteostasis|Protein transport|ER-Golgi trafficking|Anterograde transport|SAR1A/B guanine nucleotide exchange factor	mapped	ok_for_propagation_to_go	GO:0005085	guanyl-nucleotide exchange factor activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes SAR1 guanine-nucleotide exchange factors in ER export. Guanyl-nucleotide exchange factor activity captures the shared molecular function.
er_proteostasis.yaml	subtype	ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport|COPI coating and uncoating	mapped	ok_for_propagation_to_go	GO:0030126	COPI vesicle coat		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype is a COPI coat handling bucket in retrograde ER-Golgi transport. COPI vesicle coat is the appropriate shared cellular-component target.
er_proteostasis.yaml	subtype	ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport|COPI scaffolding in the Golgi	mapped	ok_for_propagation_to_go	GO:0030126	COPI vesicle coat		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes COPI coat scaffolding factors. COPI vesicle coat is the appropriate shared cellular-component target.
er_proteostasis.yaml	subtype	ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport|COPI vesicle component	mapped	ok_for_propagation_to_go	GO:0030126	COPI vesicle coat		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes COPI vesicle components. The GO COPI vesicle coat term is the direct complex target.
er_proteostasis.yaml	subtype	ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport|Receptor for KDEL-containing proteins for retrograde transport	mapped	ok_for_propagation_to_go	GO:0006890	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes KDEL receptors for Golgi-to-ER retrieval. The matching GO retrograde transport process is the appropriate propagation target.
extracellular_proteostasis.yaml	class	Extracellular proteostasis|Protease	mapped	ok_for_propagation_to_go	GO:0008233	peptidase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN class contains extracellular/intracellular proteases in the extracellular proteostasis branch. The shared molecular-function assertion is peptidase activity; narrower metallopeptidase propagation is handled by the child bucket.
extracellular_proteostasis.yaml	group	Extracellular proteostasis|Protease|Extracellular and intracellular	mapped	ok_for_propagation_to_go	GO:0004222	metalloendopeptidase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN child bucket is represented by IDE in the current taxonomy and converges on metallopeptidase biology. The GO metalloendopeptidase activity term is the clearest shared target for propagation.
extracellular_proteostasis.yaml	group	Extracellular proteostasis|Protease|Plasma membrane	mapped	ok_for_propagation_to_go	GO:0005886	plasma membrane		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures plasma-membrane-localized extracellular proteases. The source category is location-based rather than a strict GO-equivalent class, so the plasma membrane cellular-component term is used at propagation scope.
mitochondrial_proteostasis.yaml	class	Mitochondrial proteostasis|Mitochondrial protein maturation	mapped	ok_for_propagation_to_go	GO:0034982	mitochondrial protein processing		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN class groups maturation steps for mitochondrial proteins. The GO mitochondrial protein processing term captures the shared process-level semantics.
mitochondrial_proteostasis.yaml	class	Mitochondrial proteostasis|Organelle-specific protein degradation	mapped	ok_for_propagation_to_go	GO:0035694	mitochondrial protein catabolic process		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
mitochondrial_proteostasis.yaml	class	Mitochondrial proteostasis|Protein transport	mapped	ok_for_propagation_to_go	GO:0015031	protein transport		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The PN mitochondrial Protein transport class groups protein-targeting and import pathways into mitochondria. GO protein transport is the appropriate propagation target, while the source class remains mitochondria-specific and broader than any single GO transport subtype.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Chaperone|HSP100 disaggregase	mapped	ok_for_propagation_to_go	GO:0140545	ATP-dependent protein disaggregase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group denotes mitochondrial HSP100/LON-family disaggregase activity. The GO ATP-dependent protein disaggregase activity term is the closest molecular-function target.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Chaperone|Small intermembrane space chaperone	mapped	ok_for_propagation_to_go	GO:0042719	mitochondrial intermembrane space chaperone complex		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures the small intermembrane-space chaperone system that stabilizes imported proteins in the mitochondrial intermembrane space. The GO cellular-component term for the mitochondrial intermembrane space chaperone complex is an appropriate propagation target.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Chaperone|small HSP	mapped	ok_for_propagation_to_go	GO:0044183	protein folding chaperone		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group denotes mitochondrial small heat-shock chaperones. Protein folding chaperone is the appropriate shared molecular-function term.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Folding enzyme|Peptidyl-prolyl isomerases	mapped	ok_for_propagation_to_go	GO:0003755	peptidyl-prolyl cis-trans isomerase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group is the mitochondrial peptidyl-prolyl isomerase branch. The matching GO molecular-function term is appropriate for propagation.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Folding enzyme|Protein disulfide isomerases	mapped	ok_for_propagation_to_go	GO:0160203	mitochondrial disulfide relay system		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group contains CHCHD4/GFER mitochondrial disulfide-relay factors. The GO mitochondrial disulfide relay system process captures the shared mitochondrial folding chemistry better than a generic PDI label.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Membrane protein folding|Insertase for helical proteins into the outer membrane	mapped	ok_for_propagation_to_go	GO:0045040	protein insertion into mitochondrial outer membrane		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group covers the machinery that inserts helical membrane proteins into the mitochondrial outer membrane. The corresponding GO process term protein insertion into mitochondrial outer membrane is an appropriate propagation target.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Membrane protein folding|MICOS complex	mapped	ok_for_propagation_to_go	GO:0061617	MICOS complex		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group denotes MICOS-complex components. The GO MICOS complex cellular-component term is the direct target.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Membrane protein folding|Sorting and assembly machinery outer membrane	mapped	ok_for_propagation_to_go	GO:0005741	mitochondrial outer membrane		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group denotes the SAM outer-membrane assembly system. The GO mitochondrial outer membrane cellular-component term is a conservative propagation target for this assembly-focused bucket.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Mitochondrial protein maturation|Methionine deformylation	mapped	ok_for_propagation_to_go	GO:0042586	peptide deformylase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures mitochondrial N-terminal methionine deformylation. The shared catalytic activity is peptide deformylase activity.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Mitochondrial protein maturation|Processing peptidase	mapped	ok_for_propagation_to_go	GO:0017087	mitochondrial processing peptidase complex		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group captures the mitochondrial processing peptidase machinery that removes targeting presequences from imported mitochondrial proteins. The GO cellular-component term for the mitochondrial processing peptidase complex is the best supported propagation target.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Organelle-specific protein degradation|Intermembrane space protease	mapped	ok_for_propagation_to_go	GO:0005758	mitochondrial intermembrane space		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures proteases assigned specifically to the mitochondrial intermembrane space. The source bucket is compartmental and mechanistic rather than a single shared enzymatic GO class, so the mitochondrial intermembrane space cellular-component term is the conservative propagation target.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Organelle-specific protein degradation|Matrix protease	mapped	ok_for_propagation_to_go	GO:0005759	mitochondrial matrix		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group identifies matrix-local protease systems. The source is a compartmental proteostasis bucket, so the mitochondrial matrix cellular-component term is the conservative propagation target.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Protein transport|Cytosolic mitochondria import stimulation factor	mapped	ok_for_propagation_to_go	GO:0015031	protein transport		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group captures cytosolic factors that stimulate mitochondrial import before TOM/TIM route commitment. The source is broader than a specific matrix-import pathway, so the conservative propagation target is GO protein transport.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Protein transport|Inner membrane import	mapped	ok_for_propagation_to_go	GO:0045039	protein insertion into mitochondrial inner membrane		high_level_source	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, inner-membrane import is a group that covers TIM22, TIM17/23, and related inner-membrane insertion routes. The broader GO process protein insertion into mitochondrial inner membrane is therefore the correct propagation target.
mitochondrial_proteostasis.yaml	group	Mitochondrial proteostasis|Protein transport|Outer membrane import	mapped	ok_for_propagation_to_go	GO:0045040	protein insertion into mitochondrial outer membrane		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group covers the outer-membrane entry route for mitochondrial protein import. The matching GO process protein insertion into mitochondrial outer membrane is the best conservative propagation target.
mitochondrial_proteostasis.yaml	type	Mitochondrial proteostasis|Chaperone|HSP60 system|HSP10	mapped	ok_for_propagation_to_go	GO:0044183	protein folding chaperone		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes mitochondrial HSP10/HSPE co-chaperonins. The shared GO function is protein folding chaperone.
mitochondrial_proteostasis.yaml	type	Mitochondrial proteostasis|Chaperone|HSP60 system|HSP60	mapped	ok_for_propagation_to_go	GO:0140662	ATP-dependent protein folding chaperone		broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The mitochondrial HSP60 PN category corresponds to canonical chaperonins that carry out ATP-dependent protein folding. The source label denotes the family/system member type rather than the GO molecular-function class itself, so propagation scope is the better fit.
mitochondrial_proteostasis.yaml	type	Mitochondrial proteostasis|Protein transport|Inner membrane import|For assembly of inner membrane complexes	mapped	ok_for_propagation_to_go	GO:0032977	membrane insertase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN leaf is represented by OXA1L, the mitochondrial inner-membrane insertase for assembly of membrane complexes. Membrane insertase activity is the best-supported molecular-function target.
mitochondrial_proteostasis.yaml	type	Mitochondrial proteostasis|Protein transport|Inner membrane import|TIMM17/23 complex	mapped	ok_for_propagation_to_go	GO:0005744	TIM23 mitochondrial import inner membrane translocase complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type denotes TIMM17/23 import-complex components. The GO TIM23 mitochondrial import inner membrane translocase complex term is the direct cellular-component target.
mitochondrial_proteostasis.yaml	type	Mitochondrial proteostasis|Protein transport|Inner membrane import|TIMM22 complex	mapped	ok_for_propagation_to_go	GO:0042721	TIM22 mitochondrial import inner membrane insertion complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type captures TIMM22-complex components responsible for a specific inner-membrane import route. The GO cellular-component term for the TIM22 insertion complex is an appropriate propagation target.
mitochondrial_proteostasis.yaml	type	Mitochondrial proteostasis|Protein transport|Outer membrane import|TOMM complex	mapped	ok_for_propagation_to_go	GO:0005742	mitochondrial outer membrane translocase complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes TOMM-complex component membership for outer- membrane import. The source is a component-role category that maps naturally to the GO cellular-component term for the mitochondrial outer membrane translocase complex.
mitochondrial_proteostasis.yaml	subtype	Mitochondrial proteostasis|Chaperone|HSP70 system|HSP70 nucleotide exchange factor|GRPE subtype	mapped	ok_for_propagation_to_go	GO:0001405	PAM complex, Tim23 associated import motor		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This mitochondrial GRPE subtype is represented by GRPEL1/GRPEL2, PAM import-motor nucleotide-exchange factors. The GO PAM complex term is the direct complex-membership target.
nuclear_proteostasis.yaml	class	Nuclear proteostasis|Protein transport	mapped	ok_for_propagation_to_go	GO:0015031	protein transport		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The PN nuclear Protein transport class covers the machinery and routes that move proteins across the nuclear envelope. GO protein transport is the correct propagation target, although the PN class is specialized to the nuclear compartment.
nuclear_proteostasis.yaml	group	Nuclear proteostasis|Chaperone|Histone chaperone	mapped	ok_for_propagation_to_go	GO:0140713	histone chaperone activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group collects nuclear histone-chaperone factors involved in histone handling, deposition, or exchange. The PN bucket is narrower than general nuclear proteostasis and aligns well with the GO molecular function histone chaperone activity.
nuclear_proteostasis.yaml	group	Nuclear proteostasis|Protein transport|Nuclear pore complex	mapped	ok_for_propagation_to_go	GO:0005643	nuclear pore		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group denotes core components of the nuclear pore complex. The closest current GO target in the local ontology cache is the cellular-component term nuclear pore.
nuclear_proteostasis.yaml	group	Nuclear proteostasis|Protein transport|Nuclear transport receptor	mapped	ok_for_propagation_to_go	GO:0006913	nucleocytoplasmic transport		high_level_source;source_contains_domain_or_family_metadata;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group is not a clean molecular-function class. In the workbook it includes canonical karyopherin-beta transport receptors, importin-alpha cargo-recognition adaptors, and other dedicated nuclear-transport factors such as SNUPN and HIKESHI. The shared biology is participation in receptor-mediated traffic through the nuclear pore, not a single GO receptor-activity term, so the defensible target is the broader process nucleocytoplasmic transport.
nuclear_proteostasis.yaml	group	Nuclear proteostasis|Protein transport|Nuclear transport, RAN system	mapped	ok_for_propagation_to_go	GO:0006913	nucleocytoplasmic transport		high_level_source;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The PN Ran-system group captures the directionality and cargo-release machinery that powers nuclear import and export. This is a mechanistic subsystem within the broader GO process nucleocytoplasmic transport.
nuclear_proteostasis.yaml	type	Nuclear proteostasis|Protein transport|Nuclear transport receptor|Importin, alpha type	mapped	ok_for_propagation_to_go	GO:0006913	nucleocytoplasmic transport		source_contains_domain_or_family_metadata;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	Importin-alpha factors are primarily cargo-recognition adaptors that bind NLS-containing cargo and work with karyopherin-beta transport receptors, rather than forming a clean standalone GO receptor-activity class in the local ontology. The PN type is therefore better propagated to the process nucleocytoplasmic transport than forced into an MF mapping.
nuclear_proteostasis.yaml	type	Nuclear proteostasis|Protein transport|Nuclear transport receptor|Importin, beta type	mapped	ok_for_propagation_to_go	GO:0006913	nucleocytoplasmic transport		source_contains_domain_or_family_metadata;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	Importin-beta family members are the closest thing in this PN branch to a transport-receptor activity class, but the current validated GO cache does not expose a clean family-level importin/exportin receptor MF term for this mapping set. The source type is therefore propagated to the broader process nucleocytoplasmic transport.
nuclear_proteostasis.yaml	type	Nuclear proteostasis|Protein transport|Nuclear transport receptor|Non-importin transport receptor	mapped	ok_for_propagation_to_go	GO:0006913	nucleocytoplasmic transport		source_contains_domain_or_family_metadata;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type groups dedicated nuclear-transport factors outside the canonical importin-alpha/importin-beta classes, including factors such as SNUPN and HIKESHI. Because this is a mixed mechanistic bucket rather than a single shared molecular activity, propagation to nucleocytoplasmic transport is the appropriate level.
pn_regulation.yaml	class	PN regulation|Stress response integration	mapped	ok_for_propagation_to_go	GO:0006950	response to stress		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN class is an umbrella bucket for multiple stress-response axes. GO response to stress is intentionally broad but is still the most conservative propagation target for the class-level label.
pn_regulation.yaml	class	PN regulation|Transcription factor	mapped	ok_for_propagation_to_go	GO:0003700	DNA-binding transcription factor activity		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN class is the transcription-factor branch of proteostasis regulation. Current members converge on DNA-binding transcription-factor activity, making this an appropriate class-level propagation target.
pn_regulation.yaml	class	PN regulation|Translation regulator	mapped	ok_for_propagation_to_go	GO:0006417	regulation of translation		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN class is the broad translation-regulatory bucket. GO regulation of translation is the conservative propagation target for the umbrella label.
pn_regulation.yaml	group	PN regulation|Transcription factor regulator|Inflammatory response	mapped	ok_for_propagation_to_go	GO:0006954	inflammatory response		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures transcription-factor regulators assigned to inflammatory-response control. Propagation to inflammatory response keeps the source-side process context while remaining conservative about exact equivalence.
pn_regulation.yaml	group	PN regulation|Transcription factor regulator|Oxidative stress response	mapped	ok_for_propagation_to_go	GO:1900407	regulation of cellular response to oxidative stress		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group captures regulators of oxidative-stress-responsive transcription factors. Propagation to regulation of cellular response to oxidative stress preserves the intended process context.
pn_regulation.yaml	group	PN regulation|Transcription factor regulator|Unfolded protein response	mapped	ok_for_propagation_to_go	GO:0030968	endoplasmic reticulum unfolded protein response		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This regulator bucket is represented by ERN1/IRE1 signaling in the PN taxonomy. The broader ER unfolded protein response term is the appropriate propagation target for the source label.
pn_regulation.yaml	group	PN regulation|Transcription factor|Heat shock response	mapped	ok_for_propagation_to_go	GO:0034605	cellular response to heat		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	The PN group contains heat-shock transcription factors. Propagation to cellular response to heat captures the shared response program without asserting a specific target-gene set.
pn_regulation.yaml	group	PN regulation|Transcription factor|Hypoxic stress response	mapped	ok_for_propagation_to_go	GO:0071456	cellular response to hypoxia		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	The PN group contains hypoxia-response transcription factors such as HIF1A. Cellular response to hypoxia is the matching process-level target for this branch.
pn_regulation.yaml	group	PN regulation|Transcription factor|Inflammatory response	mapped	ok_for_propagation_to_go	GO:0006954	inflammatory response		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures transcription factors assigned to inflammatory response signaling as a proteostasis-regulatory context. The source is a context-defined regulator bucket rather than an exact GO-equivalent class.
pn_regulation.yaml	group	PN regulation|Transcription factor|Integrated stress response	mapped	ok_for_propagation_to_go	GO:0140467	integrated stress response signaling		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN path groups transcription factors that execute the transcriptional arm of the integrated stress response. The source category is a regulator subclass within the signaling program, so propagation to the GO ISR signaling term is appropriate.
pn_regulation.yaml	group	PN regulation|Transcription factor|Oxidative stress response	mapped	ok_for_propagation_to_go	GO:1900407	regulation of cellular response to oxidative stress		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group captures transcription factors assigned to oxidative-stress response programs. Those factors regulate the oxidative-stress response, so the GO regulation term is the appropriate propagation target.
pn_regulation.yaml	group	PN regulation|Transcription factor|Unfolded protein response	mapped	ok_for_propagation_to_go	GO:0030968	endoplasmic reticulum unfolded protein response		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	The PN group contains transcription factors that execute ER unfolded-protein-response programs. The GO ER unfolded protein response term is the conservative process target.
pn_regulation.yaml	group	PN regulation|Translation regulator|Integrated stress response	mapped	ok_for_propagation_to_go	GO:0140467	integrated stress response signaling		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN path covers translation-regulator components of the integrated stress response, including EIF2S1 phosphorylation control. These genes are participants in integrated stress response signaling, but the PN group is a mechanistic slice of the process rather than a GO-equivalent class.
pn_regulation.yaml	group	PN regulation|Translation regulator|Unfolded protein response	mapped	ok_for_propagation_to_go	GO:1903894	regulation of IRE1-mediated unfolded protein response		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group marks the translational control arm of the unfolded protein response. Regulation of IRE1-mediated unfolded protein response is the cleanest propagation target in the local GO cache.
pn_regulation.yaml	group	PN regulation|Translation regulator|microRNA	mapped	ok_for_propagation_to_go	GO:0035278	miRNA-mediated gene silencing by inhibition of translation		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group is specifically the microRNA branch under translation regulation. The matching GO process captures translational inhibition mediated by miRNAs.
pn_regulation.yaml	type	PN regulation|Transcription factor regulator|Oxidative stress response|NFE2L2 modulator	mapped	ok_for_propagation_to_go	GO:0006979	response to oxidative stress		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	NFE2L2 modulators are upstream regulators of the oxidative-stress response program. GO response to oxidative stress is the conservative propagation target here.
pn_regulation.yaml	type	PN regulation|Transcription factor regulator|Unfolded protein response|XBP1 modulator	mapped	ok_for_propagation_to_go	GO:1903894	regulation of IRE1-mediated unfolded protein response		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, XBP1 modulators are classified under transcription-factor regulators rather than translation regulators. They remain direct participants in IRE1-mediated unfolded protein response control, so the same GO regulation term is the conservative propagation target.
pn_regulation.yaml	type	PN regulation|Transcription factor|Heat shock response|Transcription of heat shock response genes	mapped	ok_for_propagation_to_go	GO:0034605	cellular response to heat		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf captures HSF-mediated heat-shock transcriptional response. The shared GO process target is cellular response to heat.
pn_regulation.yaml	type	PN regulation|Transcription factor|Hypoxic stress response|Transcription of hypoxic stress response genes	mapped	ok_for_propagation_to_go	GO:0071456	cellular response to hypoxia		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf captures HIF-mediated hypoxic transcriptional response. The shared GO process target is cellular response to hypoxia.
pn_regulation.yaml	type	PN regulation|Transcription factor|Integrated stress response|Transcription of integrated stress response genes	mapped	ok_for_propagation_to_go	GO:0140467	integrated stress response signaling		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This leaf denotes transcriptional execution of the integrated stress response. The existing ISR signaling mapping is appropriate at this narrower level as well.
pn_regulation.yaml	type	PN regulation|Transcription factor|Oxidative stress response|Transcription of oxidative response genes	mapped	ok_for_propagation_to_go	GO:1900407	regulation of cellular response to oxidative stress		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type names the transcriptional arm of the oxidative-stress response. Mapping to regulation of cellular response to oxidative stress preserves the process-level meaning without overclaiming exactness.
pn_regulation.yaml	type	PN regulation|Transcription factor|Unfolded protein response|Transcription of unfolded protein response genes	mapped	ok_for_propagation_to_go	GO:0006986	response to unfolded protein		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures transcriptional outputs of the unfolded-protein response. The broader GO response-to-unfolded-protein process is a conservative propagation target for this label.
pn_regulation.yaml	type	PN regulation|Translation regulator|Integrated stress response|Dephosphorylation of EIF2alpha/EIF2S1	mapped	ok_for_propagation_to_go	GO:0032055	negative regulation of translation in response to stress		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	EIF2S1 dephosphorylation resets the integrated stress response machinery that had imposed stress-responsive translational repression. The PN type remains part of this translation-regulatory stress module and can propagate to the same GO stress-translation term.
pn_regulation.yaml	type	PN regulation|Translation regulator|Integrated stress response|Phosphorylation of EIF2alpha/EIF2S1	mapped	ok_for_propagation_to_go	GO:0032055	negative regulation of translation in response to stress		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	EIF2S1 phosphorylation is the canonical mechanism that suppresses global translation during the integrated stress response. The GO term negative regulation of translation in response to stress is therefore an appropriate propagation target.
pn_regulation.yaml	type	PN regulation|Translation regulator|Unfolded protein response|Phosphorylation of EIF2alpha/EIF2S1	mapped	ok_for_propagation_to_go	GO:1903894	regulation of IRE1-mediated unfolded protein response		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type links eIF2alpha phosphorylation to unfolded-protein-response control. The exact GO response-to-unfolded-protein term is broader than the mechanistic subtype, so propagation to the IRE1-mediated UPR regulation term is conservative and still informative.
pn_regulation.yaml	subtype	PN regulation|Transcription factor|Inflammatory response|Transcription of xenobiotic response genes|NFkB complex component	mapped	ok_for_propagation_to_go	GO:0071159	NF-kappaB complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This subtype consists of NF-kappaB transcription-factor complex components. The GO cellular-component term NF-kappaB complex is a direct, defensible propagation target.
translation.yaml	branch	Translation	context_only	too_broad_to_propagate	GO:0006412	translation		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	The PN Translation branch is organized around the translation apparatus and immediately associated cotranslational quality-control systems. GO translation is the closest high-level process label, but the PN branch also contains adjacent machinery such as ribosome biogenesis and nascent-chain handling. Keeping this relationship is useful for interpretation, but it is too broad to project safely onto every member.
translation.yaml	class	Translation|Cytosolic translation	context_only	too_broad_to_propagate	GO:0002181	cytoplasmic translation		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	The PN class Cytosolic translation is centered on the cytoplasmic translation apparatus and process, but it also houses supporting machinery such as ribosome biogenesis factors. The GO process term is a useful high-level label for the class, but propagating it to all members would over-annotate genes whose PN placement is through assembly or maturation context rather than core cytoplasmic translation.
translation.yaml	class	Translation|Mitochondrial translation	context_only	too_broad_to_propagate	GO:0032543	mitochondrial translation		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN class is a useful mitochondrial-translation context, but it contains ribosome components, assembly factors, tRNA synthetases, regulatory factors, and translation factors. Direct propagation to mitochondrial translation would over-annotate several adjacent machinery classes, so the relationship is retained as context only.
translation.yaml	group	Translation|Cytosolic translation|Ribosome	mapped	ok_for_propagation_to_go	GO:0022626	cytosolic ribosome		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group denotes the cytosolic ribosome within the cytosolic translation branch. The more specific GO cellular-component term cytosolic ribosome is preferable to the broader ribosome term.
translation.yaml	group	Translation|Cytosolic translation|Ribosome biogenesis factor	mapped	ok_for_propagation_to_go	GO:0042254	ribosome biogenesis		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group collects factors assigned through cytosolic ribosome biogenesis, including SSU-processosome and pre-60S maturation machinery. The full PN path resolves the earlier over-annotation problem: these genes are not being placed by core translational elongation or decoding, but by assembly and maturation of ribosomal subunits. GO ribosome biogenesis is therefore the appropriate propagation target.
translation.yaml	group	Translation|Cytosolic translation|Ribosome-associated QC	mapped	ok_for_propagation_to_go	GO:0006515	protein quality control for misfolded or incompletely synthesized proteins		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The PN ribosome-associated quality-control group covers surveillance and disposal of stalled or defective nascent-chain translation products. GO lacks a dedicated ribosome-associated QC term in the local cache, so the broader protein-quality-control process is the best supported target.
translation.yaml	group	Translation|Cytosolic translation|Translation elongation	context_only	too_broad_to_propagate	GO:0006414	translational elongation		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN group is an elongation-context bucket, but it also contains tRNA synthetases, tRNA deacylases, and multisynthetase-complex members whose direct shared assertions are narrower molecular functions or complexes. The elongation relationship is retained as context only.
translation.yaml	group	Translation|Cytosolic translation|Translation initiation	mapped	ok_for_propagation_to_go	GO:0006413	translational initiation		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group denotes cytosolic translation initiation factors and complexes. Translational initiation is the shared process target.
translation.yaml	group	Translation|Cytosolic translation|Translation termination	mapped	ok_for_propagation_to_go	GO:0006415	translational termination		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group denotes cytosolic translation termination and release factors. Translational termination is the shared process target.
translation.yaml	group	Translation|Mitochondrial translation|Mitoribosome biogenesis factor	mapped	ok_for_propagation_to_go	GO:0061668	mitochondrial ribosome assembly		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group denotes factors for mitoribosome assembly and maturation. Mitochondrial ribosome assembly is the most specific shared process target.
translation.yaml	group	Translation|Mitochondrial translation|Ribosome	mapped	ok_for_propagation_to_go	GO:0005761	mitochondrial ribosome		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group denotes the mitochondrial ribosome. The GO mitochondrial ribosome cellular-component term resolves the previous deferred state.
translation.yaml	group	Translation|Mitochondrial translation|Translation elongation	context_only	too_broad_to_propagate	GO:0070125	mitochondrial translational elongation		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN group is a mitochondrial-elongation context, but it also contains mitochondrial tRNA synthetases and GatCAB amidotransferase components. The lower-level mappings capture the defensible shared functions, so this ancestor is context only.
translation.yaml	group	Translation|Mitochondrial translation|Translation initiation	mapped	ok_for_propagation_to_go	GO:0070124	mitochondrial translational initiation		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group denotes mitochondrial translation initiation machinery. The matching GO process term is appropriate for propagation.
translation.yaml	group	Translation|Mitochondrial translation|Translation termination	mapped	ok_for_propagation_to_go	GO:0070126	mitochondrial translational termination		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group denotes mitochondrial translation termination machinery. The matching GO process term is appropriate for propagation.
translation.yaml	type	Translation|Cytosolic translation|Nascent peptide husbandry|N-terminal acetylation of nascent peptide	mapped	ok_for_propagation_to_go	GO:0006474	N-terminal protein amino acid acetylation		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes N-terminal acetyltransferase machinery acting on nascent peptides. The GO N-terminal acetylation process is the direct target.
translation.yaml	type	Translation|Cytosolic translation|Nascent peptide husbandry|N-terminal methionine cleavage from nascent peptide	mapped	ok_for_propagation_to_go	GO:0004239	initiator methionyl aminopeptidase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type is represented by METAP1/METAP2. Initiator methionyl aminopeptidase activity captures the shared catalytic function.
translation.yaml	type	Translation|Cytosolic translation|Nascent peptide husbandry|N-terminal myristoylation of nascent peptide	mapped	ok_for_propagation_to_go	GO:0006499	N-terminal protein myristoylation		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes NMT-mediated nascent-chain myristoylation. The GO N-terminal protein myristoylation process is the direct target.
translation.yaml	type	Translation|Cytosolic translation|Nascent peptide husbandry|Nascent peptide chaperoning	mapped	ok_for_propagation_to_go	GO:0051083	'de novo' cotranslational protein folding		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes cotranslational chaperoning of nascent peptides. The GO de novo cotranslational protein folding term is the shared process target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome biogenesis factor|60S maturation	mapped	ok_for_propagation_to_go	GO:0000027	ribosomal large subunit assembly		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes 60S maturation factors. Ribosomal large subunit assembly captures the shared maturation process.
translation.yaml	type	Translation|Cytosolic translation|Ribosome biogenesis factor|SSU processosome	mapped	ok_for_propagation_to_go	GO:0032040	small-subunit processome		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes SSU processosome factors. The GO small-subunit processome term is the direct complex target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome biogenesis factor|pre-40S complex	mapped	ok_for_propagation_to_go	GO:0030688	preribosome, small subunit precursor		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes pre-40S particles. The GO preribosome small-subunit precursor term is the direct complex target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome biogenesis factor|pre-5S rRNA processing nuclease	mapped	ok_for_propagation_to_go	GO:0006364	rRNA processing		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes nucleases in pre-5S rRNA processing. rRNA processing is the appropriate shared process target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome biogenesis factor|pre-60S complex	mapped	ok_for_propagation_to_go	GO:0030687	preribosome, large subunit precursor		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes pre-60S particles. The GO preribosome large-subunit precursor term is the direct complex target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome biogenesis factor|pre-rRNA processing nuclease	mapped	ok_for_propagation_to_go	GO:0006364	rRNA processing		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes pre-rRNA processing nucleases. rRNA processing is the appropriate shared process target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome biogenesis factor|rRNA modification	mapped	ok_for_propagation_to_go	GO:0000154	rRNA modification		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type is a broad rRNA-modification bucket in ribosome biogenesis. GO rRNA modification captures the shared process without over-specifying methylation versus other modification chemistries.
translation.yaml	type	Translation|Cytosolic translation|Ribosome-associated QC|Deubiquitination	mapped	ok_for_propagation_to_go	GO:0101005	deubiquitinase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN RQC type denotes deubiquitinases acting in ribosome-associated quality control. Deubiquitinase activity is the shared molecular-function target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome-associated QC|O-GlcNAclyation	mapped	ok_for_propagation_to_go	GO:0006493	protein O-linked glycosylation		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN RQC type captures O-GlcNAc modification in the ribosome-associated quality-control context. Protein O-linked glycosylation is the appropriate GO process target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome-associated QC|Ribosomal rescue	mapped	ok_for_propagation_to_go	GO:0072344	rescue of stalled cytosolic ribosome		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN RQC type denotes rescue of stalled cytosolic ribosomes. The matching GO process term is the direct target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome-associated QC|UFMylation	mapped	ok_for_propagation_to_go	GO:0071569	protein ufmylation		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN RQC type denotes UFM1 conjugation in ribosome quality control. Protein ufmylation is the shared process target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome-associated QC|Ubiquitination	mapped	ok_for_propagation_to_go	GO:0016567	protein ubiquitination		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN RQC type denotes ubiquitination events on stalled translation complexes. Protein ubiquitination is the shared process target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome-associated QC|ubiquitination of eEF1A on stalled ribosomes	mapped	ok_for_propagation_to_go	GO:0016567	protein ubiquitination		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN RQC type is a specific ubiquitination bucket for eEF1A on stalled ribosomes. Protein ubiquitination is the shared process target.
translation.yaml	type	Translation|Cytosolic translation|Ribosome|Cytoribosome	mapped	ok_for_propagation_to_go	GO:0022626	cytosolic ribosome		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes cytosolic ribosome components. The GO cytosolic ribosome term is the direct cellular-component target.
translation.yaml	type	Translation|Cytosolic translation|Translation elongation|EEF1B complex	mapped	ok_for_propagation_to_go	GO:0005853	eukaryotic translation elongation factor 1 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes EEF1B complex components. The GO eukaryotic translation elongation factor 1 complex term is the direct target.
translation.yaml	type	Translation|Cytosolic translation|Translation elongation|assorted elongation factors	mapped	ok_for_propagation_to_go	GO:0003746	translation elongation factor activity		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type groups cytosolic elongation factors. Translation elongation factor activity is the shared molecular-function target.
translation.yaml	type	Translation|Cytosolic translation|Translation elongation|multisynthase complex	mapped	ok_for_propagation_to_go	GO:0017101	aminoacyl-tRNA synthetase multienzyme complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes the multisynthetase complex. The GO aminoacyl-tRNA synthetase multienzyme complex term is the direct target.
translation.yaml	type	Translation|Cytosolic translation|Translation elongation|tRNA deacylase	mapped	ok_for_propagation_to_go	GO:0002161	aminoacyl-tRNA deacylase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes tRNA deacylases. The GO aminoacyl-tRNA deacylase activity term is the direct target.
translation.yaml	type	Translation|Cytosolic translation|Translation elongation|tRNA synthetase	mapped	ok_for_propagation_to_go	GO:0004812	aminoacyl-tRNA ligase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes cytosolic aminoacyl-tRNA synthetases. The GO aminoacyl-tRNA ligase activity term is the shared molecular-function target.
translation.yaml	type	Translation|Cytosolic translation|Translation initiation|assorted initiation factors	mapped	ok_for_propagation_to_go	GO:0003743	translation initiation factor activity		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type groups cytosolic initiation factors not represented by a single named complex. Translation initiation factor activity is the shared target.
translation.yaml	type	Translation|Cytosolic translation|Translation initiation|eIF2 complex	mapped	ok_for_propagation_to_go	GO:0005850	eukaryotic translation initiation factor 2 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes component membership in the eIF2 complex. Propagation to the matching GO cellular-component term is appropriate.
translation.yaml	type	Translation|Cytosolic translation|Translation initiation|eIF2B complex	mapped	ok_for_propagation_to_go	GO:0005851	eukaryotic translation initiation factor 2B complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes component membership in the eIF2B complex. The corresponding GO cellular-component term is an appropriate propagation target.
translation.yaml	type	Translation|Cytosolic translation|Translation initiation|eIF3 complex	mapped	ok_for_propagation_to_go	GO:0005852	eukaryotic translation initiation factor 3 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes component membership in the eIF3 complex. Propagation to the matching GO cellular-component term is appropriate.
translation.yaml	type	Translation|Cytosolic translation|Translation initiation|eIF4F complex	mapped	ok_for_propagation_to_go	GO:0016281	eukaryotic translation initiation factor 4F complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes eIF4F complex components. The GO eukaryotic translation initiation factor 4F complex term resolves the previous deferred state.
translation.yaml	type	Translation|Cytosolic translation|Translation termination|Polypeptide release	mapped	ok_for_propagation_to_go	GO:0003747	translation release factor activity		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes release factors that mediate polypeptide release. Translation release factor activity is the shared molecular-function target.
translation.yaml	type	Translation|Cytosolic translation|Translation termination|Stop codon recognition	mapped	ok_for_propagation_to_go	GO:0016149	translation release factor activity, codon specific		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes codon-specific stop-codon recognition by release factors. The GO codon-specific release-factor activity term is the direct target.
translation.yaml	type	Translation|Mitochondrial translation|Mitoribosome biogenesis factor|28S subunit assembly	mapped	ok_for_propagation_to_go	GO:0061668	mitochondrial ribosome assembly		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes 28S mitoribosomal subunit assembly factors. Mitochondrial ribosome assembly is the shared process target.
translation.yaml	type	Translation|Mitochondrial translation|Mitoribosome biogenesis factor|28S subunit rRNA modification	mapped	ok_for_propagation_to_go	GO:0000154	rRNA modification		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes modification of mitochondrial small-subunit rRNA. GO rRNA modification captures the shared process without over-specifying methylation versus other modification chemistries.
translation.yaml	type	Translation|Mitochondrial translation|Mitoribosome biogenesis factor|39S subunit assembly	mapped	ok_for_propagation_to_go	GO:0061668	mitochondrial ribosome assembly		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes 39S mitoribosomal subunit assembly factors. Mitochondrial ribosome assembly is the shared process target.
translation.yaml	type	Translation|Mitochondrial translation|Mitoribosome biogenesis factor|39S subunit rRNA modification	mapped	ok_for_propagation_to_go	GO:0000154	rRNA modification		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes modification of mitochondrial large-subunit rRNA. GO rRNA modification captures the shared process without over-specifying methylation versus other modification chemistries.
translation.yaml	type	Translation|Mitochondrial translation|Ribosome|Mitoribosome	mapped	ok_for_propagation_to_go	GO:0005761	mitochondrial ribosome		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes mitoribosome components. The GO mitochondrial ribosome term is the direct cellular-component target.
translation.yaml	type	Translation|Mitochondrial translation|Translation elongation|Amidotransferase complex	mapped	ok_for_propagation_to_go	GO:0030956	glutamyl-tRNA(Gln) amidotransferase complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes the mitochondrial GatCAB amidotransferase complex. The GO glutamyl-tRNA(Gln) amidotransferase complex term is the direct target.
translation.yaml	type	Translation|Mitochondrial translation|Translation elongation|assorted elongation factors	mapped	ok_for_propagation_to_go	GO:0003746	translation elongation factor activity		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type groups mitochondrial elongation factors. Translation elongation factor activity is the shared molecular-function target.
translation.yaml	type	Translation|Mitochondrial translation|Translation elongation|tRNA synthetase	mapped	ok_for_propagation_to_go	GO:0004812	aminoacyl-tRNA ligase activity		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes mitochondrial aminoacyl-tRNA synthetases. The GO aminoacyl-tRNA ligase activity term is the shared molecular-function target.
translation.yaml	type	Translation|Mitochondrial translation|Translation initiation|assorted initiation factors	mapped	ok_for_propagation_to_go	GO:0003743	translation initiation factor activity		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type groups mitochondrial initiation factors. Translation initiation factor activity is the shared molecular-function target.
translation.yaml	type	Translation|Mitochondrial translation|Translation termination|Normal termination	mapped	ok_for_propagation_to_go	GO:0070126	mitochondrial translational termination		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes normal mitochondrial translation termination. The GO mitochondrial translational termination process is the shared target.
translation.yaml	type	Translation|Mitochondrial translation|Translation termination|Termination on stalled ribosomes	mapped	ok_for_propagation_to_go	GO:7770016	rescue of stalled mitochondrial ribosome		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes handling of stalled mitochondrial ribosomes. The GO rescue of stalled mitochondrial ribosome process is the best matching target.
translation.yaml	subtype	Translation|Cytosolic translation|Nascent peptide husbandry|Nascent peptide chaperoning|RAC component	mapped	ok_for_propagation_to_go	GO:0051083	'de novo' cotranslational protein folding		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The ribosome-associated complex is a cotranslational chaperone system for emerging nascent chains. The PN subtype is a specific component class within this mechanism, so propagation to GO 'de novo' cotranslational protein folding is justified but not exact.
translation.yaml	subtype	Translation|Cytosolic translation|Nascent peptide husbandry|Nascent peptide sorting|NAC component	mapped	ok_for_propagation_to_go	GO:0005854	nascent polypeptide-associated complex		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes NAC components. The GO nascent polypeptide-associated complex term is the direct complex target.
translation.yaml	subtype	Translation|Cytosolic translation|Ribosome|Cytoribosome|40S subunit	mapped	ok_for_propagation_to_go	GO:0022627	cytosolic small ribosomal subunit		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes 40S cytosolic ribosomal subunit components. The GO cytosolic small ribosomal subunit term is the direct target.
translation.yaml	subtype	Translation|Cytosolic translation|Ribosome|Cytoribosome|60S subunit	mapped	ok_for_propagation_to_go	GO:0022625	cytosolic large ribosomal subunit		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes 60S cytosolic ribosomal subunit components. The GO cytosolic large ribosomal subunit term is the direct target.
translation.yaml	subtype	Translation|Mitochondrial translation|Mitoribosome biogenesis factor|39S subunit rRNA modification|rRNA pseudouridylation	mapped	ok_for_propagation_to_go	GO:0120159	rRNA pseudouridine synthase activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes mitochondrial rRNA pseudouridylation factors. rRNA pseudouridine synthase activity is the shared molecular-function target.
translation.yaml	subtype	Translation|Mitochondrial translation|Ribosome|Mitoribosome|28S subunit	mapped	ok_for_propagation_to_go	GO:0005763	mitochondrial small ribosomal subunit		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes 28S mitochondrial small ribosomal subunit components. The GO mitochondrial small ribosomal subunit term is the direct target.
translation.yaml	subtype	Translation|Mitochondrial translation|Ribosome|Mitoribosome|39S subunit	mapped	ok_for_propagation_to_go	GO:0005762	mitochondrial large ribosomal subunit		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype denotes 39S mitochondrial large ribosomal subunit components. The GO mitochondrial large ribosomal subunit term is the direct target.
translation.yaml	subtype	Translation|Mitochondrial translation|Translation elongation|Amidotransferase complex|Conversion of Glu-tRNA(Gln) to Gln-tRNA(Gln)	mapped	ok_for_propagation_to_go	GO:0030956	glutamyl-tRNA(Gln) amidotransferase complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype is the GatCAB-mediated conversion of Glu-tRNA(Gln) to Gln-tRNA(Gln). The GO amidotransferase complex term is the direct shared target.
ubiquitin_proteasome_system.yaml	class	Ubiquitin Proteasome System|E1 activating enzymes	context_only	too_broad_to_propagate	GO:0008641	ubiquitin-like modifier activating enzyme activity		high_level_source;too_broad_to_propagate	context_only_not_projected	This class is a real ubiquitin-like modifier E1 context, but it spans ubiquitin, SUMO, NEDD8, UFM1, URM1, ISG15, FAT10, and autophagy modifiers. Propagation is safer from the curated child groups.
ubiquitin_proteasome_system.yaml	class	Ubiquitin Proteasome System|E2 conjugating enzymes	context_only	too_broad_to_propagate	GO:0019787	ubiquitin-like protein transferase activity		high_level_source;too_broad_to_propagate	context_only_not_projected	This class is a real E2/UBL transferase context, but it includes ubiquitin, SUMO, NEDD8, UFMylation, ATGylation, dual-use, and inactive buckets. Propagation is restricted to narrower curated children.
ubiquitin_proteasome_system.yaml	class	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases	context_only	too_broad_to_propagate	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	This class is a genuine E3-ligase context, but its descendants include catalytic ligases, cullin scaffolds, substrate receptors, adaptors, cofactors, regulators, and UBL modifier systems. A class-level propagation would over-annotate.
ubiquitin_proteasome_system.yaml	class	Ubiquitin Proteasome System|Proteasome and associated proteins	context_only	too_broad_to_propagate	GO:0000502	proteasome complex		high_level_source;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	This class records the proteasome branch context, but descendants include core and regulatory particle subunits, activators, assembly chaperones, adaptors, DUBs, E3 ligases, enzymes, and transcriptional regulators. Propagation should come from narrower nodes.
ubiquitin_proteasome_system.yaml	class	Ubiquitin Proteasome System|Ubiquitin and UBL binding	context_only	too_broad_to_propagate	GO:0140036	ubiquitin-modified protein reader activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	This class records ubiquitin/UBL-reader context, but the subtree mixes ubiquitin, SUMO, UBL-domain, domain-architecture, catalytic, signaling, trafficking, and nucleic-acid process buckets. It is useful context, not a safe direct propagation.
ubiquitin_proteasome_system.yaml	class	Ubiquitin Proteasome System|Ubiquitin and UBL proteins	context_only	too_broad_to_propagate	GO:0019787	ubiquitin-like protein transferase activity		high_level_source;source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	This class groups ubiquitin, UBL modifiers, UBX/UBL-domain proteins, and UBL-containing enzymes. The branch is UPS-relevant but too mixed to propagate as a single GO annotation.
ubiquitin_proteasome_system.yaml	class	Ubiquitin Proteasome System|VCP and associated proteins	context_only	too_broad_to_propagate	GO:0043335	protein unfolding		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This class records the VCP segregase branch context, but descendants include VCP, substrate adaptors, DUBs, E3 ligases, channels, and unrelated associated enzymes. Direct propagation is restricted to narrower nodes.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|ATG4 cysteine protease	mapped	ok_for_propagation_to_go	GO:0008234	cysteine-type peptidase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is the ATG4 cysteine protease family. The shared defensible GO assertion is cysteine-type peptidase activity; autophagy-specific ATG8 processing is curated in the ALP branch.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|BRISC complex	mapped	ok_for_propagation_to_go	GO:0070552	BRISC complex		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group denotes BRISC complex members. The matching GO cellular-component term is BRISC complex.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|CSN complex	mapped	ok_for_propagation_to_go	GO:0008180	COP9 signalosome		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group denotes COP9 signalosome/CSN complex members. The matching GO cellular-component term is COP9 signalosome.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|Josephin	mapped	ok_for_propagation_to_go	GO:0101005	deubiquitinase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is an active deubiquitinase family bucket. The shared molecular-function assertion is deubiquitinase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|MINDY	mapped	ok_for_propagation_to_go	GO:0101005	deubiquitinase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is an active deubiquitinase family bucket. The shared molecular-function assertion is deubiquitinase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|OTU	context_only	too_broad_to_propagate	GO:0101005	deubiquitinase activity		high_level_source;source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	This OTU-family group is DUB-related context, but the subtree includes inactive or ambiguous OTU-like cases. Direct DUB propagation should come from narrower gene-level review rather than this whole family bucket.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|UCH	mapped	ok_for_propagation_to_go	GO:0101005	deubiquitinase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is an active deubiquitinase family bucket. The shared molecular-function assertion is deubiquitinase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|UFSP	mapped	ok_for_propagation_to_go	GO:0071567	deUFMylase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group captures UFSP-family deUFMylases. The matching GO molecular-function term is deUFMylase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|USP	mapped	ok_for_propagation_to_go	GO:0101005	deubiquitinase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is an active deubiquitinase family bucket. The shared molecular-function assertion is deubiquitinase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|DUBs and UBL demodifiers|ZUP1	mapped	ok_for_propagation_to_go	GO:0101005	deubiquitinase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is an active deubiquitinase family bucket. The shared molecular-function assertion is deubiquitinase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E1 activating enzymes|activation of ATG8, ATG12	mapped	ok_for_propagation_to_go	GO:0019778	Atg12 activating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures the autophagy-related E1 activation step for ATG8 and ATG12 family members. The GO Atg12 activating enzyme activity term is the specific propagation target supported by the local ontology cache.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E1 activating enzymes|activation of ISG15	mapped	ok_for_propagation_to_go	GO:0008641	ubiquitin-like modifier activating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group represents E1 activation of the ubiquitin-like modifier ISG15. The generic GO ubiquitin-like modifier activating enzyme activity term is the appropriate propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E1 activating enzymes|activation of NEDD8	mapped	ok_for_propagation_to_go	GO:0008641	ubiquitin-like modifier activating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group represents E1 activation of the ubiquitin-like modifier NEDD8. The generic GO activating enzyme activity term is the safest propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E1 activating enzymes|activation of SUMO	mapped	ok_for_propagation_to_go	GO:0008641	ubiquitin-like modifier activating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group represents E1 activation of the SUMO modifier family. The generic GO activating enzyme activity term is the safest propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E1 activating enzymes|activation of UFM1	mapped	ok_for_propagation_to_go	GO:0008641	ubiquitin-like modifier activating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group represents E1 activation of the UFM1 modifier family. The generic GO activating enzyme activity term is the safest propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E1 activating enzymes|activation of URM1	mapped	ok_for_propagation_to_go	GO:0008641	ubiquitin-like modifier activating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group represents E1 activation of the ubiquitin-like modifier URM1. The generic GO activating enzyme activity term is the safest propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E1 activating enzymes|activation of ubiquitin	mapped	ok_for_propagation_to_go	GO:0008641	ubiquitin-like modifier activating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures the canonical ubiquitin E1 activation step. The GO ubiquitin-like modifier activating enzyme activity term is the best propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E1 activating enzymes|activation of ubiquitin and FAT10	mapped	ok_for_propagation_to_go	GO:0008641	ubiquitin-like modifier activating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group represents E1 activation of ubiquitin-family modifiers. The generic GO ubiquitin-like modifier activating enzyme activity term is the appropriate propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E2 conjugating enzymes|ATGylation	context_only	too_broad_to_propagate	GO:0019787	ubiquitin-like protein transferase activity		high_level_source;too_broad_to_propagate	context_only_not_projected	This group captures ATG3/ATG10-like autophagy conjugation enzymes, but ATG8 and ATG12 conjugation require different precise terms. The group is kept as UBL-transferase context and should not propagate directly.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E2 conjugating enzymes|FAT10ylation	mapped	ok_for_propagation_to_go	GO:0019787	ubiquitin-like protein transferase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group is a UBL-conjugating E2 bucket. The safest shared molecular-function target is ubiquitin-like protein transferase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E2 conjugating enzymes|NEDDylation	mapped	ok_for_propagation_to_go	GO:0019788	NEDD8 transferase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures NEDD8-conjugating E2 enzymes. The matching GO molecular-function term is NEDD8 transferase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E2 conjugating enzymes|SUMOylation	mapped	ok_for_propagation_to_go	GO:0019789	SUMO transferase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures SUMO-conjugating E2 enzymes. The local GO cache provides SUMO transferase activity as the closest supported molecular- function target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E2 conjugating enzymes|UFMylation	mapped	ok_for_propagation_to_go	GO:0019787	ubiquitin-like protein transferase activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group is a UBL-conjugating E2 bucket. The safest shared molecular-function target is ubiquitin-like protein transferase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group captures canonical ubiquitin E2 enzymes. The GO molecular- function term ubiquitin conjugating enzyme activity is the appropriate propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination, ISG15ylation	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		high_level_source	manual_gene_level_review_required_before_gene_review_change	This PN group contains dual ubiquitin/ISG15 E2 enzymes. Ubiquitin conjugating enzyme activity is the shared GO molecular-function target supported for this bucket.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|CRL regulator	context_only	too_broad_to_propagate	GO:1904666	regulation of ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN group records regulation of cullin-RING ligase systems, but the members include inhibitors, exchange factors, and modulators with different directionality. It is context only.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul1 substrate adaptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul1 substrate receptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul2 substrate adaptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul2 substrate receptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul3 substrate adaptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul3 substrate receptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul4A/Cul4B receptor scaffold	mapped	ok_for_propagation_to_go	GO:0160072	ubiquitin ligase complex scaffold activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group captures cullin or cullin-associated scaffold roles in ubiquitin ligase complexes. The shared GO molecular-function target is ubiquitin ligase complex scaffold activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul4A/Cul4B substrate adaptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul4A/Cul4B substrate receptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul7 substrate receptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cullin	mapped	ok_for_propagation_to_go	GO:0160072	ubiquitin ligase complex scaffold activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group captures cullin or cullin-associated scaffold roles in ubiquitin ligase complexes. The shared GO molecular-function target is ubiquitin ligase complex scaffold activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cullin adaptor	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|E3 with intrinsic E2	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is a catalytic ubiquitin E3 ligase bucket. The shared GO molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|HECT	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is a catalytic ubiquitin E3 ligase bucket. The shared GO molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|RBR	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is a catalytic ubiquitin E3 ligase bucket. The shared GO molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|RBX RING	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is a catalytic ubiquitin E3 ligase bucket. The shared GO molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|RCR	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is a catalytic ubiquitin E3 ligase bucket. The shared GO molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|RING	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is a catalytic ubiquitin E3 ligase bucket. The shared GO molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|RING variant	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is a catalytic ubiquitin E3 ligase bucket. The shared GO molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|RZ	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is a catalytic ubiquitin E3 ligase bucket. The shared GO molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|UBL modifiers	context_only	too_broad_to_propagate	GO:0019787	ubiquitin-like protein transferase activity		high_level_source;source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	This group records UBL-modifier ligase context, but descendants include cofactors and idiosyncratic SUMOylation/ATGylation entries that are not uniformly transferase activities. Keep as context only.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|idiosyncratic E3	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is a catalytic ubiquitin E3 ligase bucket. The shared GO molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|idiosyncratic E3 ligase complex	mapped	ok_for_propagation_to_go	GO:0000151	ubiquitin ligase complex		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is an E3 ligase complex bucket. The safest shared GO target is ubiquitin ligase complex membership rather than assigning catalytic activity to every subunit.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|idiosyncratic RBR complex	mapped	ok_for_propagation_to_go	GO:0000151	ubiquitin ligase complex		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is an E3 ligase complex bucket. The safest shared GO target is ubiquitin ligase complex membership rather than assigning catalytic activity to every subunit.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|idiosyncratic RING complex	mapped	ok_for_propagation_to_go	GO:0000151	ubiquitin ligase complex		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is an E3 ligase complex bucket. The safest shared GO target is ubiquitin ligase complex membership rather than assigning catalytic activity to every subunit.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|idiosyncratic UBOX complex	mapped	ok_for_propagation_to_go	GO:0000151	ubiquitin ligase complex		high_level_source;source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group is an E3 ligase complex bucket. The safest shared GO target is ubiquitin ligase complex membership rather than assigning catalytic activity to every subunit.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Proteasome and associated proteins|adaptors	mapped	ok_for_propagation_to_go	GO:0070628	proteasome binding		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group captures proteasome adaptors and shuttle factors. Proteasome binding is the safe shared molecular-function target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Proteasome and associated proteins|associated DUB	mapped	ok_for_propagation_to_go	GO:0101005	deubiquitinase activity		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures proteasome-associated deubiquitinases. The shared molecular-function target is deubiquitinase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Proteasome and associated proteins|associated E3 ligase	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures proteasome-associated E3 ligases. The shared molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome activators and inhibitors	context_only	too_broad_to_propagate	GO:0070628	proteasome binding		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN group mixes proteasome activators, inhibitors, and broader modulators. The proteasome relationship is real, but direct propagation should come from narrower activator/modulator nodes.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome assembly chaperone	mapped	ok_for_propagation_to_go	GO:0043248	proteasome assembly		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures proteasome assembly chaperones. The shared GO biological-process target is proteasome assembly.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome core particle subunit	mapped	ok_for_propagation_to_go	GO:0005839	proteasome core complex		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures proteasome core particle subunits. The matching GO cellular-component term is proteasome core complex.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome regulatory particle subunit	mapped	ok_for_propagation_to_go	GO:0005838	proteasome regulatory particle		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures proteasome regulatory particle subunits. The matching GO cellular-component term is proteasome regulatory particle.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|DNA repair	mapped	ok_for_propagation_to_go	GO:0006281	DNA repair		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group captures ubiquitin/UBL-binding factors assigned to DNA repair contexts. The group is context-defined rather than GO-equivalent, but propagation to DNA repair is appropriate.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|DNA replication	mapped	ok_for_propagation_to_go	GO:0006260	DNA replication		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group is defined by ubiquitin/UBL-binding roles in DNA replication. The source category is narrower than the GO process itself and is therefore treated as a propagation mapping.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|DUB	context_only	too_broad_to_propagate	GO:0101005	deubiquitinase activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	This UBL-binding group is DUB-related context, but it includes noncatalytic or pseudo-DUB domain cases such as NPLOC4/USP39-like entries. Active DUB propagation is handled from the DUB-family branch.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|DUB & E3 ligase	context_only	too_broad_to_propagate	GO:0101005	deubiquitinase activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	This PN group is a dual DUB/E3 ligase bucket. The DUB relationship is real, but one GO target cannot capture both activities without losing information.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|E2 conjugating enzyme	context_only	too_broad_to_propagate	GO:0061631	ubiquitin conjugating enzyme activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	This UBL-binding group contains E2 enzymes/domain contexts rather than a clean E2-binding activity bucket. E2 catalytic propagation is handled in the E2 conjugating enzyme branch.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|E2 conjugating enzyme for SUMO	mapped	ok_for_propagation_to_go	GO:0019789	SUMO transferase activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group identifies the SUMO E2 conjugating enzyme bucket. The matching GO molecular-function target is SUMO transferase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|E3 ligase	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures ubiquitin/UBL-binding factors that are E3 ligases. The shared molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|E3 ligase / UBLM	context_only	too_broad_to_propagate	GO:0019787	ubiquitin-like protein transferase activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	This binding-branch group records E3/UBL-modifier context, but it includes cofactors as well as catalytic ligases. Direct propagation should come from narrower enzyme-specific nodes.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|E3 ligase complex component	mapped	ok_for_propagation_to_go	GO:0000151	ubiquitin ligase complex		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures E3 ligase complex components. The safe shared GO target is ubiquitin ligase complex membership.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|E3 ligase inhibitor	mapped	ok_for_propagation_to_go	GO:1990948	ubiquitin ligase inhibitor activity		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures UPS factors that inhibit E3 ligases. The matching GO activity term ubiquitin ligase inhibitor activity is the best supported propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|VCP and proteasome adaptor	mapped	ok_for_propagation_to_go	GO:0070628	proteasome binding		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group captures proteasome adaptor/shuttle factors. Proteasome binding is the safe shared molecular-function target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|mRNA export	mapped	ok_for_propagation_to_go	GO:0016973	poly(A)+ mRNA export from nucleus		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group is a direct mRNA-export context bucket within the UPS branch. The GO mRNA export term is the specific target supported by the local ontology cache.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|mitotic exit and cytokinesis	mapped	ok_for_propagation_to_go	GO:0000281	mitotic cytokinesis		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group is a direct mitotic-exit/cytokinesis context bucket within the UPS branch. The GO mitotic cytokinesis process is the appropriate propagation target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|nuclear pore complex subunit	mapped	ok_for_propagation_to_go	GO:0005643	nuclear pore		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures ubiquitin/UBL-binding nuclear pore complex subunits. The matching GO cellular-component term is nuclear pore.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|proteasomal subunits	mapped	ok_for_propagation_to_go	GO:0000502	proteasome complex		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures ubiquitin/UBL-binding proteasomal subunits. The shared GO target is proteasome complex.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|proteasome adaptor	mapped	ok_for_propagation_to_go	GO:0070628	proteasome binding		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group captures proteasome adaptor/shuttle factors. Proteasome binding is the safe shared molecular-function target.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|protein quality control	context_only	too_broad_to_propagate	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN group is a protein-quality-control context bucket, but its descendants include ERAD cofactors, HSP70 cochaperone context, stalled-chain recognition, and other mixed roles. Direct propagation should come from narrower nodes such as ERAD cofactor.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL binding|translation	context_only	too_broad_to_propagate	GO:0006412	translation		high_level_source;source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN group captures ubiquitin/UBL-binding factors assigned to translation-related contexts. The relationship to translation is real, but the group mixes heterogeneous subcontexts including repression, nascent-peptide binding, ribosome maturation, and ribosome-quality- control-adjacent roles.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain	context_only	too_broad_to_propagate	GO:0043130	ubiquitin binding		high_level_source;source_contains_domain_or_family_metadata;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This group records UBL-domain protein context, but descendants include enzymes, adaptors, chaperone-related proteins, non-enzymatic proteins, and nucleic-acid factors. Propagation is restricted to narrower nodes.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|VCP and associated proteins|VCP	mapped	ok_for_propagation_to_go	GO:0043335	protein unfolding		high_level_source;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN group is the VCP/p97 segregase node. The defensible shared GO target for VCP itself is protein unfolding.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|VCP and associated proteins|adaptors	context_only	too_broad_to_propagate	GO:0034098	VCP-NPL4-UFD1 AAA ATPase complex		high_level_source;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	This PN group records VCP adaptor context, but it mixes UBX, SHP, VIM, VBM, membrane, and other adaptor classes. Direct propagation should come only from narrower complex-specific nodes or gene-level review.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|VCP and associated proteins|associated DUBs	context_only	too_broad_to_propagate	GO:0101005	deubiquitinase activity		high_level_source;source_is_regulatory_or_contextual;too_broad_to_propagate	context_only_not_projected	This VCP-associated group is DUB-related context, but it includes NPLOC4 complex membership as well as catalytic DUBs. Direct DUB propagation comes from the DUB-family branch or narrower reviewed nodes.
ubiquitin_proteasome_system.yaml	group	Ubiquitin Proteasome System|VCP and associated proteins|associated E3 ligases	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		high_level_source;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN group captures VCP-associated E3 ligases. The shared molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|BRISC complex|catalytic subunit	mapped	ok_for_propagation_to_go	GO:0140492	metal-dependent deubiquitinase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type is the catalytic JAMM/MPN subunit of the BRISC complex. The shared molecular function is metal-dependent deubiquitinase activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|BRISC complex|noncatalytic	mapped	ok_for_propagation_to_go	GO:0070552	BRISC complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type covers noncatalytic BRISC subunits, so complex membership is the safe propagation target rather than catalytic DUB activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|CSN complex|deNEDDylase	mapped	ok_for_propagation_to_go	GO:0008180	COP9 signalosome		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type covers COP9 signalosome members assigned to the deNEDDylase complex. Complex membership is safe for all members, whereas deNEDDylase activity is not safe for every subunit.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|JAMM / MPN|CSN complex	mapped	ok_for_propagation_to_go	GO:0008180	COP9 signalosome		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN group denotes COP9 signalosome/CSN complex members. The matching GO cellular-component term is COP9 signalosome.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|JAMM / MPN|EIF3 complex	mapped	ok_for_propagation_to_go	GO:0005852	eukaryotic translation initiation factor 3 complex		source_contains_domain_or_family_metadata;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type captures JAMM/MPN proteins assigned to the eIF3 complex, notably proteostasis-linked eIF3 subunits with metalloprotease-like MPN domains. The GO eIF3 complex term is the correct propagation target.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|JAMM / MPN|USP dimerization domain	mapped	ok_for_propagation_to_go	GO:0140492	metal-dependent deubiquitinase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type groups catalytically active JAMM/MPN metalloprotease DUBs. The shared molecular-function target is metal-dependent deubiquitinase activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|JAMM / MPN|assorted	mapped	ok_for_propagation_to_go	GO:0140492	metal-dependent deubiquitinase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type groups catalytically active JAMM/MPN metalloprotease DUBs. The shared molecular-function target is metal-dependent deubiquitinase activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|JAMM / MPN|proteasomal	mapped	ok_for_propagation_to_go	GO:0140492	metal-dependent deubiquitinase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type captures the proteasomal JAMM/MPN deubiquitinase PSMD14/RPN11 context. The shared molecular-function target is metal-dependent deubiquitinase activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|SENP|deNEDDylase, NEDD8 processing	mapped	ok_for_propagation_to_go	GO:0019784	deNEDDylase activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type is the SENP8/NEDD8-processing bucket. The matching GO molecular-function term is deNEDDylase activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|DUBs and UBL demodifiers|UFSP|deUFMylase	mapped	ok_for_propagation_to_go	GO:0071567	deUFMylase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type is the explicit deUFMylase bucket under UFSP proteins. The matching GO molecular-function term is deUFMylase activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|CRL regulator|CRL inhibitor	mapped	ok_for_propagation_to_go	GO:1904667	negative regulation of ubiquitin protein ligase activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type captures cullin-RING ligase inhibitors. The matching GO process target is negative regulation of ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|CRL regulator|F-box exchange factor	mapped	ok_for_propagation_to_go	GO:1990757	ubiquitin ligase activator activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures CAND-family exchange factors that activate/remodel cullin-RING ligase assemblies. The closest shared GO activity is ubiquitin ligase activator activity.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|idiosyncratic RBR complex|LUBAC	mapped	ok_for_propagation_to_go	GO:0000151	ubiquitin ligase complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type denotes the LUBAC RBR E3 ligase complex. The safe GO propagation target is ubiquitin ligase complex.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|idiosyncratic RING complex|Anaphase Promoting Complex	mapped	ok_for_propagation_to_go	GO:0005680	anaphase-promoting complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, APC/C is nested under the idiosyncratic RING-complex branch rather than appearing as a direct group. The GO cellular-component term anaphase-promoting complex remains the appropriate propagation target.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|idiosyncratic RING complex|BRCA1-A complex	mapped	ok_for_propagation_to_go	GO:0070531	BRCA1-A complex		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN type denotes BRCA1-A complex members. The matching GO cellular-component term is BRCA1-A complex.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome activators and inhibitors|activator, AAA	mapped	ok_for_propagation_to_go	GO:0070628	proteasome binding		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the proteasome activator bucket is now the AAA-type activator subtype under proteasome activators and inhibitors. The local GO cache does not expose a proteasome-activator activity term, so proteasome binding is the most conservative supported target.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome activators and inhibitors|modulator	mapped	ok_for_propagation_to_go	GO:0070628	proteasome binding		source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	The earlier inhibitor bucket is no longer present in `4.3.11`; the surviving coarse category is proteasome modulator. The local GO cache lacks a specific proteasome-modulator activity term, so proteasome binding is the conservative propagation target.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome assembly chaperone|core particle	mapped	ok_for_propagation_to_go	GO:0043248	proteasome assembly		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes assembly chaperones for the proteasome core particle. The GO proteasome assembly process is the appropriate propagation target.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome assembly chaperone|regulatory particle	mapped	ok_for_propagation_to_go	GO:0043248	proteasome assembly		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type denotes assembly chaperones for the proteasome regulatory particle. The local GO cache does not expose a regulatory-particle assembly term, so the broader proteasome assembly process is the correct conservative target.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome core particle subunit|alpha subunit	mapped	ok_for_propagation_to_go	GO:0019773	proteasome core complex, alpha-subunit complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures alpha-subunit proteasome core members. The matching GO cellular-component term is proteasome core complex, alpha-subunit complex.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome core particle subunit|beta subunit	mapped	ok_for_propagation_to_go	GO:0019774	proteasome core complex, beta-subunit complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures beta-subunit proteasome core members. The matching GO cellular-component term is proteasome core complex, beta-subunit complex.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome regulatory particle subunit|base, ATPase	mapped	ok_for_propagation_to_go	GO:0008540	proteasome regulatory particle, base subcomplex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures base subunits of the proteasome regulatory particle. The matching GO cellular-component term is proteasome regulatory particle, base subcomplex.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome regulatory particle subunit|base, nonATPase	mapped	ok_for_propagation_to_go	GO:0008540	proteasome regulatory particle, base subcomplex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures base subunits of the proteasome regulatory particle. The matching GO cellular-component term is proteasome regulatory particle, base subcomplex.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Proteasome and associated proteins|proteasome regulatory particle subunit|lid, nonATPase	mapped	ok_for_propagation_to_go	GO:0008541	proteasome regulatory particle, lid subcomplex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures lid subunits of the proteasome regulatory particle. The matching GO cellular-component term is proteasome regulatory particle, lid subcomplex.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL binding|mRNA maturation|mRNA splicing	mapped	ok_for_propagation_to_go	GO:0048024	regulation of mRNA splicing, via spliceosome		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type is a direct mRNA-splicing context bucket within the UPS branch. The GO splicing-regulation term is the supported propagation target in the local cache.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL binding|other DNA dependent processes|chromatin remodeling	mapped	ok_for_propagation_to_go	GO:0006338	chromatin remodeling		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type groups ubiquitin/UBL-binding factors assigned to chromatin remodeling. The source is a context bucket rather than a canonical GO class, so propagation scope is appropriate.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL binding|proteasomal subunits|regulatory particle	mapped	ok_for_propagation_to_go	GO:0005838	proteasome regulatory particle		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type/subtype is a ubiquitin-binding regulatory-particle subunit bucket. The safe GO target is proteasome regulatory particle.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL binding|protein kinases & regulators|GATOR2 complex	mapped	ok_for_propagation_to_go	GO:0061700	GATOR2 complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type identifies ubiquitin/UBL-binding factors assigned to the GATOR2 complex. The GO cellular-component term GATOR2 complex is an appropriate propagation target.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL binding|protein quality control|ERAD cofactor	mapped	ok_for_propagation_to_go	GO:0097466	ubiquitin-dependent glycoprotein ERAD pathway		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type groups ubiquitin/UBL-binding factors that act as ERAD cofactors in protein-quality-control contexts. The best available GO target in the local cache is ubiquitin-dependent glycoprotein ERAD pathway, used here at propagation scope.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL binding|trafficking|macroautophagy	context_only	too_broad_to_propagate	GO:0016236	macroautophagy		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN type is an autophagy-related trafficking context, but the earlier TRAPP review showed that generic autophagy propagation from component or binding-context buckets can be too strong. Keep as context unless gene-level evidence supports macroautophagy.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL binding|trafficking|mitophagy	context_only	too_broad_to_propagate	GO:0000423	mitophagy		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target;too_broad_to_propagate	context_only_not_projected	This PN type records a mitophagy-related trafficking context. The relationship is biologically real, but automatic mitophagy propagation from a UPS binding bucket is too strong without gene-level review.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL binding|trafficking|phospholipid binding	mapped	ok_for_propagation_to_go	GO:0005543	phospholipid binding		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes ubiquitin/UBL-binding factors additionally assigned to phospholipid binding in trafficking contexts. The matching GO molecular function is a reasonable propagation target.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL binding|transcription|DNA binding	mapped	ok_for_propagation_to_go	GO:0003677	DNA binding		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type groups ubiquitin/UBL-binding factors assigned to transcriptional DNA-binding contexts. Propagation to GO DNA binding is appropriate, with the caveat that the PN source is context-defined.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|DUB	context_only	too_broad_to_propagate	GO:0101005	deubiquitinase activity		source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	This UBL-domain type is DUB-related context, but the subtree includes noncatalytic MPN/UBL-domain cases. Active DUB propagation is handled from the DUB-family branch.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|E3 ligases	context_only	too_broad_to_propagate	GO:0061630	ubiquitin protein ligase activity		source_contains_domain_or_family_metadata;too_broad_to_propagate	context_only_not_projected	This UBL-domain type is an E3-ligase context, but descendants include catalytic E3s as well as cullin receptor/adaptor components. Direct propagation is restricted to narrower subtypes.
ubiquitin_proteasome_system.yaml	type	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|ubiquitin binding	mapped	ok_for_propagation_to_go	GO:0043130	ubiquitin binding		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN type denotes UBL-domain proteins assigned to ubiquitin-binding roles. The matching GO molecular-function term ubiquitin binding is the correct propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 11|UBC domain & C-terminal extension	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, this architecture appears as a family-specific subtype under the ubiquitination group. The structural specialization does not change the core E2 molecular function.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 12|UBC domain & N-terminal extension	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, this architecture appears as a family-specific subtype under the ubiquitination group. The N-terminal extension does not change the core E2 activity assignment.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 13|UBC domain only	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the minimal UBC-domain architecture appears as a family-specific subtype beneath the ubiquitination group. The core GO activity term remains the correct propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 14|E2-E3 chimera	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, E2 architectural variants are modeled as family-specific subtypes beneath the ubiquitination group. This condition-scoped subtype mapping preserves the original intent across any family carrying the E2-E3 chimera architecture.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 15|UBC domain only	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the minimal UBC-domain architecture appears as a family-specific subtype beneath the ubiquitination group. The core GO activity term remains the correct propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 17 homolog|UBC domain only	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the minimal UBC-domain architecture appears as a family-specific subtype beneath the ubiquitination group. The core GO activity term remains the correct propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 2|UBC domain only	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the minimal UBC-domain architecture appears as a family-specific subtype beneath the ubiquitination group. The core GO activity term remains the correct propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 3|UBC domain & C-terminal extension	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, this architecture appears as a family-specific subtype under the ubiquitination group. The structural specialization does not change the core E2 molecular function.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 3|UBC domain only	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the minimal UBC-domain architecture appears as a family-specific subtype beneath the ubiquitination group. The core GO activity term remains the correct propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 4|UBC domain & C-terminal extension	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, this architecture appears as a family-specific subtype under the ubiquitination group. The structural specialization does not change the core E2 molecular function.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 4|UBC domain & N-terminal extension	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, this architecture appears as a family-specific subtype under the ubiquitination group. The N-terminal extension does not change the core E2 activity assignment.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 4|UBC domain only	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the minimal UBC-domain architecture appears as a family-specific subtype beneath the ubiquitination group. The core GO activity term remains the correct propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 5|UBC domain & transmembrane domain	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, this membrane-anchored architecture appears as a family-specific subtype beneath the ubiquitination group. The structural specialization does not change the core conjugating activity.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 6|UBC domain & C-terminal extension	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, this architecture appears as a family-specific subtype under the ubiquitination group. The structural specialization does not change the core E2 molecular function.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 9|UBC domain & C-terminal extension	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, this architecture appears as a family-specific subtype under the ubiquitination group. The structural specialization does not change the core E2 molecular function.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E2 conjugating enzymes|ubiquitination|Family 9|UBC domain only	mapped	ok_for_propagation_to_go	GO:0061631	ubiquitin conjugating enzyme activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the minimal UBC-domain architecture appears as a family-specific subtype beneath the ubiquitination group. The core GO activity term remains the correct propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|CRL regulator|F-box exchange factor|Armadillo-like	mapped	ok_for_propagation_to_go	GO:1990757	ubiquitin ligase activator activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type captures CAND-family exchange factors that activate/remodel cullin-RING ligase assemblies. The closest shared GO activity is ubiquitin ligase activator activity.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL binding|other DNA dependent processes|chromatin remodeling|idiosyncratic Ub binding / other	mapped	ok_for_propagation_to_go	GO:0006338	chromatin remodeling		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	In `4.3.11`, the residual chromatin-remodeling subgroup is labeled idiosyncratic Ub binding / other rather than just idiosyncratic. The parent chromatin-remodeling GO term remains the safest propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL binding|proteasomal subunits|regulatory particle|UIM, idiosyncratic Ub binding / VWA	mapped	ok_for_propagation_to_go	GO:0005838	proteasome regulatory particle		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type/subtype is a ubiquitin-binding regulatory-particle subunit bucket. The safe GO target is proteasome regulatory particle.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL binding|proteasomal subunits|regulatory particle|idiosyncratic Ub binding / MPN	mapped	ok_for_propagation_to_go	GO:0005838	proteasome regulatory particle		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type/subtype is a ubiquitin-binding regulatory-particle subunit bucket. The safe GO target is proteasome regulatory particle.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL binding|proteasomal subunits|regulatory particle|idiosyncratic Ub binding / PRU	mapped	ok_for_propagation_to_go	GO:0005838	proteasome regulatory particle		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type/subtype is a ubiquitin-binding regulatory-particle subunit bucket. The safe GO target is proteasome regulatory particle.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL binding|proteasomal subunits|regulatory particle|idiosyncratic Ub binding / alpha solenoid	mapped	ok_for_propagation_to_go	GO:0005838	proteasome regulatory particle		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN type/subtype is a ubiquitin-binding regulatory-particle subunit bucket. The safe GO target is proteasome regulatory particle.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|E3 ligases|CUL1 receptor / F-box	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN subtype identifies a UBL-domain F-box/CUL1 receptor role. The safe shared molecular function is ubiquitin-like ligase-substrate adaptor activity rather than catalytic E3 activity.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|E3 ligases|Cullin adaptor / Elongin B	mapped	ok_for_propagation_to_go	GO:1990756	ubiquitin-like ligase-substrate adaptor activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype identifies a UBL-domain cullin-adaptor role. The safe shared molecular function is ubiquitin-like ligase-substrate adaptor activity rather than catalytic E3 activity.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|E3 ligases|RBR / LUBAC complex	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN node identifies UBL-domain proteins that are E3 ligases. The shared molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|E3 ligases|RBR / Parkin	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN node identifies UBL-domain proteins that are E3 ligases. The shared molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|E3 ligases|RING / RAWUL / polycomb	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN node identifies UBL-domain proteins that are E3 ligases. The shared molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|E3 ligases|RING / UHRF	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		source_contains_domain_or_family_metadata	manual_gene_level_review_required_before_gene_review_change	This PN node identifies UBL-domain proteins that are E3 ligases. The shared molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|E3 ligases|RING / other	mapped	ok_for_propagation_to_go	GO:0061630	ubiquitin protein ligase activity		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN node identifies UBL-domain proteins that are E3 ligases. The shared molecular-function target is ubiquitin protein ligase activity.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|non-enzymatic|actin binding	mapped	ok_for_propagation_to_go	GO:0003779	actin binding		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype captures non-enzymatic UBL-domain proteins assigned to actin-binding roles. The matching GO activity term is suitable for propagation.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|nucleic acid processes|DNA repair	mapped	ok_for_propagation_to_go	GO:0006281	DNA repair		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual;broad_or_context_loss_target	manual_gene_level_review_required_before_gene_review_change	This PN subtype groups UBL-domain proteins in nucleic-acid-process contexts that are assigned to DNA repair. Propagation to DNA repair is appropriate.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|Ubiquitin and UBL proteins|UBL domain|nucleic acid processes|double-stranded RNA binding	mapped	ok_for_propagation_to_go	GO:0003725	double-stranded RNA binding		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype captures UBL-domain proteins assigned to double-stranded RNA binding. The matching GO molecular-function term is an appropriate propagation target.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|VCP and associated proteins|adaptors|SHP|UT3	mapped	ok_for_propagation_to_go	GO:0034098	VCP-NPL4-UFD1 AAA ATPase complex		source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype identifies UFD1 in the canonical VCP-NPL4-UFD1 adaptor complex. The matching GO cellular-component term is VCP-NPL4-UFD1 AAA ATPase complex.
ubiquitin_proteasome_system.yaml	subtype	Ubiquitin Proteasome System|VCP and associated proteins|associated DUBs|MPN|UBXL	mapped	ok_for_propagation_to_go	GO:0034098	VCP-NPL4-UFD1 AAA ATPase complex		source_contains_domain_or_family_metadata;source_is_regulatory_or_contextual	manual_gene_level_review_required_before_gene_review_change	This PN subtype identifies NPLOC4 in the VCP-NPL4-UFD1 complex context. The safe GO target is VCP-NPL4-UFD1 AAA ATPase complex, not DUB activity.