id: pn_mapping_set:er_proteostasis label: ER proteostasis PN mappings references: - proteostasis-workbook-2024 - proteostasis-ms1 notes: >- Curated PN-to-GO mappings for ER proteostasis, including glycoproteostasis, ERAD, and transport. subject_curations: - subject_code: ER proteostasis subject_level: branch curation_status: no_mapping rationale: Reviewed as a top-level PN branch. This is a systems/taxonomy umbrella, not a direct GO assertion; narrower child curations carry any propagating GO mappings. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone subject_level: class curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Folding enzyme subject_level: class curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Glycoproteostasis subject_level: class curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Maturation and folding of specific substrates subject_level: class curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation subject_level: class curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport subject_level: class curation_status: mapped target_term: id: GO:0015031 label: protein transport mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - file:human/BAG6/BAG6-ai-review.yaml - file:human/BAG6/BAG6-notes.md - PMID:20676083 - PMID:25535373 excluded_subjects: - condition_level: gene_symbol condition_code: BAG6 notes: >- BAG6 is excluded after gene-level review because its GET-pathway placement is already captured by narrower tail-anchored/ER-targeting terms, including post-translational protein targeting to endoplasmic reticulum membrane. Propagating the broad parent protein-transport term would add less precise context rather than a useful new assertion. - subject_code: ER proteostasis|Chaperone|Chaperone for MCT1-4 subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|Chaperone for various receptors subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP70 system subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP90 system subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Folding enzyme|Peptidyl-prolyl isomerases subject_level: group curation_status: mapped target_term: id: GO:0003755 label: peptidyl-prolyl cis-trans isomerase activity mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Folding enzyme|Peroxiredoxins subject_level: group curation_status: mapped target_term: id: GO:0051920 label: peroxiredoxin activity mapping_scope: ok_for_propagation_to_go rationale: This PN group denotes ER peroxiredoxins. The shared molecular function is peroxiredoxin activity. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Folding enzyme|Protein disulfide isomerases subject_level: group curation_status: mapped target_term: id: GO:0003756 label: protein disulfide isomerase activity mapping_scope: ok_for_propagation_to_go rationale: >- This PN group captures the canonical ER protein-disulfide-isomerase folding enzymes. GO protein disulfide isomerase activity is the cleanest propagation target for the catalytically active family members. references: - proteostasis-workbook-2024 - proteostasis-ms1 - file:human/ERP27/ERP27-ai-review.yaml - file:human/ERP29/ERP29-ai-review.yaml excluded_subjects: - condition_level: gene_symbol condition_code: ERP27 - condition_level: gene_symbol condition_code: ERP29 - condition_level: gene_symbol condition_code: ERO1A - condition_level: gene_symbol condition_code: ERO1B notes: >- ERP27 and ERP29 are excluded from GO:0003756 propagation after gene-level review (proteostasis batch 5). Both are PDI-family ER-resident proteins that LACK the redox-active thioredoxin CXXC active-site motif and therefore have no protein-disulfide-isomerase catalytic activity: ERP27 is a non-catalytic substrate-binding partner that presents unfolded clients to PDIA3/ERp57, and ERP29 is a non-catalytic homodimeric escort/chaperone. Both reviews carry NOT|protein-disulfide-isomerase-activity annotations. ERO1A and ERO1B are also excluded from this group-level GO:0003756 propagation: they are FAD-dependent sulfhydryl OXIDASES that reoxidize PDI, not isomerases (their gene reviews flag the PDI/reductase terms as over-annotations). They retain the corrected molecular function GO:0016971 (flavin-dependent sulfhydryl oxidase activity) via the child "Protein disulfide isomerase reoxidation" type node; the parent PDI-activity term must not propagate to them. Inheriting GO:0003756 from this group would over-annotate these escort chaperones and oxidases; their genuine roles are captured at the gene level. The catalytic isomerase members (e.g. P4HB/PDI, PDIA3, PDIA4, PDIA6) retain the mapping, and DNAJC10/ERdj5 (a thioredoxin- family reductase) is also retained. - subject_code: ER proteostasis|Glycoproteostasis|N-glycosylation system subject_level: group curation_status: mapped target_term: id: GO:0006487 label: protein N-linked glycosylation mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - file:human/CLGN/CLGN-ai-review.yaml - file:human/CALR3/CALR3-ai-review.yaml excluded_subjects: - condition_level: type condition_code: ER proteostasis|Glycoproteostasis|N-glycosylation system|Lectin chaperone notes: >- The Lectin chaperone type (calnexin/calreticulin family: CANX, CALR, CLGN, CALR3) is excluded after gene-level review. These members bind monoglucosylated N-glycans as molecular chaperones but do not catalyze N-linked glycosylation, so inheriting the catalytic process term GO:0006487 from this group overstates their function. Gene reviews of the testis lectin chaperones CLGN (calmegin) and CALR3 (calreticulin-3) confirmed protein folding / chaperone roles with no glycosyltransferase activity. The enzymatic members of this group (oligosaccharyltransferase complex components) retain the GO:0006487 propagation via the narrower type-level mappings. - subject_code: ER proteostasis|Glycoproteostasis|O-glycosylation system subject_level: group curation_status: mapped target_term: id: GO:0006493 label: protein O-linked glycosylation mapping_scope: ok_for_propagation_to_go rationale: This PN group captures ER O-glycosylation machinery. Protein O-linked glycosylation is the appropriate shared process target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Maturation and folding of specific substrates|ER collagen processing and folding subject_level: group curation_status: mapped target_term: id: GO:0032964 label: collagen biosynthetic process mapping_scope: ok_for_propagation_to_go rationale: This PN group contains ER factors dedicated to collagen maturation, processing, and folding. Collagen biosynthetic process captures the shared substrate-specific pathway context. references: - proteostasis-workbook-2024 - proteostasis-ms1 - file:human/SERPINH1/SERPINH1-ai-review.yaml - file:human/PPIB/PPIB-ai-review.yaml - file:human/P4HB/P4HB-ai-review.yaml notes: >- Confirmed by gene-level review (proteostasis batch 5): SERPINH1/HSP47 is a collagen-specific ER molecular chaperone, PPIB/cyclophilin B is the ER peptidyl-prolyl isomerase that catalyzes collagen prolyl isomerization (with the P3H1/CRTAP complex), and P4HB/PDI serves as the structural beta-subunit of prolyl 4-hydroxylase. All three support the shared collagen-biogenesis process context at propagation scope. (Note that the substrate-specific process term is the appropriate shared mapping; member-specific molecular functions such as PPIase activity, collagen binding, and PDI activity are captured at the gene level.) - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation subject_level: group curation_status: mapped target_term: id: GO:0036503 label: ERAD pathway mapping_scope: exact rationale: >- 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. references: - proteostasis-workbook-2024 notes: >- This starter mapping targets the generic ERAD pathway term rather than more specific glycoprotein-ERAD descendants. - subject_code: ER proteostasis|Protein transport|ER signal peptidase subject_level: group curation_status: mapped target_term: id: GO:0005787 label: signal peptidase complex mapping_scope: ok_for_propagation_to_go rationale: This PN group denotes ER signal peptidase complex components. The matching GO cellular-component term is the direct propagation target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|GET pathway component subject_level: group curation_status: mapped target_term: id: GO:0006620 label: post-translational protein targeting to endoplasmic reticulum membrane mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - file:human/SGTA/SGTA-ai-review.yaml notes: >- Confirmed by gene-level review (proteostasis batch 5): SGTA is a small glutamine-rich TPR cochaperone that acts in the BAG6/TRC40-GET pathway, functioning as a molecular adaptor in the targeting and quality control of tail-anchored membrane proteins for insertion into the ER membrane, consistent with this post-translational ER-targeting process mapping. - subject_code: ER proteostasis|Protein transport|Removal of misinserted transmembrane proteins subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|SEC61 channel accessory protein subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|SEC61 channel complex component subject_level: group curation_status: mapped target_term: id: GO:0005784 label: Sec61 translocon complex mapping_scope: ok_for_propagation_to_go rationale: This PN group denotes SEC61 translocon components. The GO Sec61 translocon complex term is the direct cellular-component target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|SRP receptor subunit subject_level: group curation_status: mapped target_term: id: GO:0006614 label: SRP-dependent cotranslational protein targeting to membrane mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|Signal recognition particle component subject_level: group curation_status: mapped target_term: id: GO:0006614 label: SRP-dependent cotranslational protein targeting to membrane mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|TRAP complex component subject_level: group curation_status: no_mapping rationale: Reviewed as a narrower taxonomy bucket already covered by a curated parent mapping or by gene-level annotations. No additional direct GO mapping is appropriate from this node. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|Transmembrane protein import subject_level: group curation_status: mapped target_term: id: GO:0044743 label: protein transmembrane import into intracellular organelle mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP70 system|HSP70 activity modulator subject_level: type curation_status: no_mapping rationale: Reviewed as a contextual PN bucket. The label is useful for curator triage, but no direct GO mapping is appropriate because propagation would add a process, activity, or localization not shared cleanly by all members. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP70 system|HSP70 nucleotide exchange inhibitor subject_level: type curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP70 system|non-JDP HSP70 cochaperone subject_level: type curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP90 system|HSP90 cochaperone subject_level: type curation_status: mapped target_term: id: GO:0051879 label: Hsp90 protein binding mapping_scope: ok_for_propagation_to_go rationale: This PN type groups ER HSP90/GRP94 cochaperones. Hsp90 protein binding is the shared mechanistic assertion. references: - proteostasis-workbook-2024 - proteostasis-ms1 - file:human/CNPY3/CNPY3-ai-review.yaml notes: >- Gene-level review of CNPY3 (PRAT4A) confirmed this propagation: it is an ER co-chaperone that binds HSP90B1/GRP94 to fold and traffic Toll-like receptors, and the review assigned Hsp90 protein binding (GO:0051879). - subject_code: ER proteostasis|Folding enzyme|Peptidyl-prolyl isomerases|Cyclophilin type subject_level: type curation_status: mapped target_term: id: GO:0003755 label: peptidyl-prolyl cis-trans isomerase activity mapping_scope: ok_for_propagation_to_go rationale: This PN type denotes ER cyclophilin-family PPIases. The matching GO molecular function is appropriate for propagation. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Folding enzyme|Peptidyl-prolyl isomerases|FKBP type subject_level: type curation_status: mapped target_term: id: GO:0003755 label: peptidyl-prolyl cis-trans isomerase activity mapping_scope: ok_for_propagation_to_go rationale: This PN type denotes ER FKBP-family PPIases. The matching GO molecular function is appropriate for propagation. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- ER proteostasis|Folding enzyme|Protein disulfide isomerases|Protein disulfide isomerase reoxidation subject_level: type curation_status: mapped target_term: id: GO:0016971 label: flavin-dependent sulfhydryl oxidase activity mapping_scope: ok_for_propagation_to_go rationale: >- Corrected after gene-level review (proteostasis batch 5). This PN type is the ERO1 "PDI reoxidation" step, whose members (ERO1A/ERO1L, ERO1B/ERO1LB) are FAD-dependent sulfhydryl OXIDASES that reoxidize PDI to regenerate its active site — they do not themselves catalyze protein disulfide isomerization. The previous target GO:0003756 (protein disulfide isomerase activity) was incorrect for this node and would mislabel the oxidases as isomerases (both ERO1A and ERO1B reviews mark the protein-disulfide reductase/isomerase terms as over-annotations). The correct shared molecular function is GO:0016971 flavin-dependent sulfhydryl oxidase activity, which both genes carry with experimental (EXP) evidence in GOA. references: - proteostasis-workbook-2024 - proteostasis-ms1 - file:human/ERO1A/ERO1A-ai-review.yaml - file:human/ERO1B/ERO1B-ai-review.yaml - subject_code: ER proteostasis|Glycoproteostasis|N-glycosylation system|Lectin chaperone subject_level: type curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Glycoproteostasis|N-glycosylation system|N-glycan processing subject_level: type curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Glycoproteostasis|N-glycosylation system|Oligosaccharyl transferase complex component subject_level: type curation_status: mapped target_term: id: GO:0008250 label: oligosaccharyltransferase complex mapping_scope: ok_for_propagation_to_go rationale: This PN type denotes oligosaccharyltransferase complex components. The GO complex term is the direct cellular-component target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Glycoproteostasis|O-glycosylation system|O-mannosylation subject_level: type curation_status: mapped target_term: id: GO:0006493 label: protein O-linked glycosylation mapping_scope: ok_for_propagation_to_go rationale: This PN type captures ER O-mannosylation machinery. Current GO support is best represented by the broader protein O-linked glycosylation process. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates subject_level: type curation_status: mapped target_term: id: GO:0036503 label: ERAD pathway mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- ER proteostasis|Organelle-specific protein degradation|ER associated degradation|ER handling of ERAD substrates subject_level: type curation_status: mapped target_term: id: GO:0036503 label: ERAD pathway mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Retrotranslocation channel complex subject_level: type curation_status: no_mapping rationale: Reviewed as a narrower taxonomy bucket already covered by a curated parent mapping or by gene-level annotations. No additional direct GO mapping is appropriate from this node. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- ER proteostasis|Organelle-specific protein degradation|ER associated degradation|VCP system for retrotranslocation in ERAD subject_level: type curation_status: mapped target_term: id: GO:0036503 label: ERAD pathway mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking|Antero- and retrograde transport subject_level: type curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking|Anterograde transport subject_level: type curation_status: mapped target_term: id: GO:0006888 label: endoplasmic reticulum to Golgi vesicle-mediated transport mapping_scope: ok_for_propagation_to_go rationale: This PN type captures anterograde ER-to-Golgi trafficking factors. The GO ER-to-Golgi vesicle-mediated transport process is the shared target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport subject_level: type curation_status: mapped target_term: id: GO:0006890 label: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|Transmembrane protein import|BOS complex component subject_level: type curation_status: no_mapping rationale: Reviewed as a narrower taxonomy bucket already covered by a curated parent mapping or by gene-level annotations. No additional direct GO mapping is appropriate from this node. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|Transmembrane protein import|EMC complex component subject_level: type curation_status: mapped target_term: id: GO:0072546 label: EMC complex mapping_scope: ok_for_propagation_to_go rationale: This PN type denotes ER membrane protein complex components. The GO EMC complex cellular-component term is the direct target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|Transmembrane protein import|GEL complex component subject_level: type curation_status: no_mapping rationale: Reviewed as a narrower taxonomy bucket already covered by a curated parent mapping or by gene-level annotations. No additional direct GO mapping is appropriate from this node. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|Transmembrane protein import|PAT complex component subject_level: type curation_status: mapped target_term: id: GO:0160005 label: PAT complex mapping_scope: ok_for_propagation_to_go rationale: This PN type denotes PAT-complex components in ER membrane protein insertion. The GO PAT complex term is the direct target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP70 system|HSP70 nucleotide exchange factor|HSP110/GRP170 subtype subject_level: subtype curation_status: no_mapping rationale: Reviewed as a family/domain/subtype label. It classifies PN members but is not itself a GO annotation target; functional assertions should come from a parent role mapping or gene-specific review. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP70 system|HSP70 nucleotide exchange factor|HSPBP1 subtype subject_level: subtype curation_status: no_mapping rationale: Reviewed as a family/domain/subtype label. It classifies PN members but is not itself a GO annotation target; functional assertions should come from a parent role mapping or gene-specific review. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP70 system|HSP70 nucleotide exchange inhibitor|SAP subtype subject_level: subtype curation_status: no_mapping rationale: Reviewed as a family/domain/subtype label. It classifies PN members but is not itself a GO annotation target; functional assertions should come from a parent role mapping or gene-specific review. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP90 system|HSP90 cochaperone|Folding of IGM and IgA subject_level: subtype curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Chaperone|HSP90 system|HSP90 cochaperone|Folding of TLRs subject_level: subtype curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Glycoproteostasis|N-glycosylation system|N-glycan processing|Glucose trimming subject_level: subtype curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- ER proteostasis|Glycoproteostasis|N-glycosylation system|N-glycan processing|Mannose trimming subject_level: subtype curation_status: mapped target_term: id: GO:1904382 label: mannose trimming involved in glycoprotein ERAD pathway mapping_scope: ok_for_propagation_to_go rationale: >- 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. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Glycoproteostasis|N-glycosylation system|N-glycan processing|Re-glucosylation subject_level: subtype curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|Deglycosylation of ERAD substrates subject_level: subtype curation_status: mapped target_term: id: GO:0006517 label: protein deglycosylation mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes cytosolic deglycosylation of ERAD substrates. Protein deglycosylation is the appropriate shared process target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated DUB subject_level: subtype curation_status: mapped target_term: id: GO:0101005 label: deubiquitinase activity mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes ERAD-associated deubiquitinases. Deubiquitinase activity captures the shared molecular function. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated E2 conjugating enzyme subject_level: subtype curation_status: mapped target_term: id: GO:0061631 label: ubiquitin conjugating enzyme activity mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes ERAD-associated E2 enzymes. Ubiquitin conjugating enzyme activity is the appropriate shared molecular-function target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated RING E3 ligase subject_level: subtype curation_status: mapped target_term: id: GO:0061630 label: ubiquitin protein ligase activity mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes ERAD-associated RING E3 ligases. Ubiquitin protein ligase activity is the appropriate shared catalytic target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated UBOX E3 ligase subject_level: subtype curation_status: mapped target_term: id: GO:0061630 label: ubiquitin protein ligase activity mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes ERAD-associated U-box E3 ligases. Ubiquitin protein ligase activity is the appropriate shared catalytic target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated UPS component subject_level: subtype curation_status: no_mapping rationale: Reviewed as a narrower taxonomy bucket already covered by a curated parent mapping or by gene-level annotations. No additional direct GO mapping is appropriate from this node. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|Cytosolic handling of ERAD substrates|ERAD-associated idiosyncratic E3 ligase subject_level: subtype curation_status: mapped target_term: id: GO:0061630 label: ubiquitin protein ligase activity mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes ERAD-associated E3 ligases with noncanonical architecture. Ubiquitin protein ligase activity is the shared catalytic target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|VCP system for retrotranslocation in ERAD|Intramembrane protease, cleaves unstable membrane proteins, transfers to ERAD subject_level: subtype curation_status: mapped target_term: id: GO:0004252 label: serine-type endopeptidase activity mapping_scope: ok_for_propagation_to_go rationale: This PN subtype is represented by rhomboid-family intramembrane proteases. Serine-type endopeptidase activity is the shared catalytic target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|VCP system for retrotranslocation in ERAD|VCP subject_level: subtype curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Organelle-specific protein degradation|ER associated degradation|VCP system for retrotranslocation in ERAD|VCP accessories subject_level: subtype curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking|Antero- and retrograde transport|Cargo receptor subject_level: subtype curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking|Anterograde transport|COPII vesicle component subject_level: subtype curation_status: mapped target_term: id: GO:0030127 label: COPII vesicle coat mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes COPII vesicle coat components. The GO COPII vesicle coat term is the direct complex target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking|Anterograde transport|SAR1A/B guanine nucleotide exchange factor subject_level: subtype curation_status: mapped target_term: id: GO:0005085 label: guanyl-nucleotide exchange factor activity mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes SAR1 guanine-nucleotide exchange factors in ER export. Guanyl-nucleotide exchange factor activity captures the shared molecular function. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport|COPI coating and uncoating subject_level: subtype curation_status: mapped target_term: id: GO:0030126 label: COPI vesicle coat mapping_scope: ok_for_propagation_to_go rationale: This PN subtype is a COPI coat handling bucket in retrograde ER-Golgi transport. COPI vesicle coat is the appropriate shared cellular-component target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport|COPI scaffolding in the Golgi subject_level: subtype curation_status: mapped target_term: id: GO:0030126 label: COPI vesicle coat mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes COPI coat scaffolding factors. COPI vesicle coat is the appropriate shared cellular-component target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport|COPI vesicle component subject_level: subtype curation_status: mapped target_term: id: GO:0030126 label: COPI vesicle coat mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes COPI vesicle components. The GO COPI vesicle coat term is the direct complex target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: ER proteostasis|Protein transport|ER-Golgi trafficking|Retrograde transport|Receptor for KDEL-containing proteins for retrograde transport subject_level: subtype curation_status: mapped target_term: id: GO:0006890 label: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum mapping_scope: ok_for_propagation_to_go rationale: This PN subtype denotes KDEL receptors for Golgi-to-ER retrieval. The matching GO retrograde transport process is the appropriate propagation target. references: - proteostasis-workbook-2024 - proteostasis-ms1