# Hand-curated RGD Pathway Ontology -> GO biological process mappings (SSSOM). # Edit this file by hand; analyze_rgd_pathways.py merges it into the generated set # (pw_go_mappings.sssom.yaml, curation_rule pw2go:src/CURATED_MAPPING) and stops with # an error if a GO id is missing, obsolete, not a biological process, or mislabelled. # Validate with: just validate-rgd-mappings # # Predicates follow SSSOM/SKOS: the object (GO) relative to the subject (PW). # exactMatch, closeMatch and narrowMatch rows are used for GO-CAM and module matching. # broadMatch and relatedMatch rows, and rows to sssom:NoTermFound, are recorded but not # used for matching: a broad GO term would match every module under it. mapping_set_id: https://w3id.org/ai4curation/ai-gene-review/mappings/pw2go-curated mapping_set_title: RGD Pathway Ontology to GO biological process curated mappings mapping_set_description: >- Curator mappings for the RGD diagram pathways that the generated PW -> GO candidate set left without a GO biological process mapping. Each row was chosen by comparing the PW definition with GO term definitions in the GO release named in summary.yaml. license: https://creativecommons.org/licenses/by/4.0/ creator_label: - AI Gene Review project mapping_date: '2026-10-26' subject_source: PW object_source: GO curie_map: PW: http://purl.obolibrary.org/obo/PW_ GO: http://purl.obolibrary.org/obo/GO_ skos: http://www.w3.org/2004/02/skos/core# semapv: https://w3id.org/semapv/vocab/ sssom: https://w3id.org/sssom/ mappings: - subject_id: PW:0001338 subject_label: histone modification pathway predicate_id: skos:exactMatch object_id: sssom:NoTermFound mapping_justification: semapv:ManualMappingCuration comment: >- GO obsoleted GO:0016570 histone modification and its children; histone-modifying steps are now captured as molecular functions under GO:0140993 histone modifying activity, with no replacement process term. - subject_id: PW:0001140 subject_label: calcium/calcium-mediated signaling pathway predicate_id: skos:narrowMatch object_id: GO:0019722 object_label: calcium-mediated signaling mapping_justification: semapv:ManualMappingCuration comment: >- GO:0019722 is intracellular signalling via calcium ions; the PW pathway also covers calcium as a first messenger and calcium transport. - subject_id: PW:0001073 subject_label: spliceosome pathway predicate_id: skos:narrowMatch object_id: GO:0000398 object_label: mRNA splicing, via spliceosome mapping_justification: semapv:ManualMappingCuration comment: >- The PW definition is spliceosomal removal of introns to give mature mRNA, including alternative splicing; it also covers lncRNA splicing, which GO:0000398 does not, so the GO term is narrower. - subject_id: PW:0000639 subject_label: insulin responsive facilitative sugar transporter mediated glucose transport pathway predicate_id: skos:closeMatch object_id: GO:0044381 object_label: glucose import in response to insulin stimulus mapping_justification: semapv:ManualMappingCuration comment: The PW pathway is insulin-stimulated GLUT4 (SLC2A4) glucose uptake. - subject_id: PW:0000543 subject_label: protein kinase A (PKA) signaling pathway predicate_id: skos:closeMatch object_id: GO:0141156 object_label: cAMP/PKA signal transduction mapping_justification: semapv:ManualMappingCuration comment: >- Both run from adenylyl-cyclase cAMP production through PKA to its effectors. PW's own citation, GO:0010737 protein kinase A signaling, is obsolete without a replacement. - subject_id: PW:0000492 subject_label: renin-angiotensin cascade pathway predicate_id: skos:closeMatch object_id: GO:0002003 object_label: angiotensin maturation mapping_justification: semapv:ManualMappingCuration comment: >- The cascade is the proteolytic generation of the angiotensin peptides from angiotensinogen. Signalling by those peptides is the separate PW:0000244 angiotensin II signaling pathway. - subject_id: PW:0000492 subject_label: renin-angiotensin cascade pathway predicate_id: skos:relatedMatch object_id: GO:0003081 object_label: regulation of systemic arterial blood pressure by renin-angiotensin mapping_justification: semapv:ManualMappingCuration comment: The physiological outcome GO names for the renin-angiotensin system. - subject_id: PW:0000718 subject_label: p53 signaling pathway predicate_id: skos:closeMatch object_id: GO:0072331 object_label: signal transduction by p53 class mediator mapping_justification: semapv:ManualMappingCuration - subject_id: PW:0001361 subject_label: ataxia telangiectasia-mutated (ATM) signaling pathway predicate_id: skos:broadMatch object_id: GO:0042770 object_label: signal transduction in response to DNA damage mapping_justification: semapv:ManualMappingCuration comment: >- The PW pathway is ATM signalling from double-strand breaks. GO has no double-strand-break-specific or ATM-specific signalling term. - subject_id: PW:0001361 subject_label: ataxia telangiectasia-mutated (ATM) signaling pathway predicate_id: skos:narrowMatch object_id: GO:0000077 object_label: DNA damage checkpoint signaling mapping_justification: semapv:ManualMappingCuration comment: >- The checkpoint arm of ATM signalling; the PW pathway also triggers repair and apoptosis. GO:0000077 also covers ATR-dependent checkpoint signalling, so a GO-CAM matched through it may be an ATR model (for example 65039e8700000123) rather than an ATM one. - subject_id: PW:0001587 subject_label: mRNA nuclear export pathway predicate_id: skos:exactMatch object_id: GO:0006406 object_label: mRNA export from nucleus mapping_justification: semapv:ManualMappingCuration - subject_id: PW:0000244 subject_label: angiotensin II signaling pathway predicate_id: skos:closeMatch object_id: GO:0038166 object_label: angiotensin-activated signaling pathway mapping_justification: semapv:ManualMappingCuration comment: GO:0038166 is defined as GPCR signalling initiated by angiotensin II. - subject_id: PW:0002581 subject_label: nicotinamide adenine nucleotide utilization pathway predicate_id: skos:closeMatch object_id: GO:0019677 object_label: NAD+ catabolic process mapping_justification: semapv:ManualMappingCuration comment: >- The PW pathway is NAD+ consumption as a substrate by sirtuins, ADP-ribosyl transferases and NAD glycohydrolases (CD38, BST1), which breaks NAD+ down. - subject_id: PW:0001185 subject_label: calcium/calmodulin dependent kinase 2 signaling pathway predicate_id: skos:broadMatch object_id: GO:0019722 object_label: calcium-mediated signaling mapping_justification: semapv:ManualMappingCuration comment: >- GO obsoleted GO:0099004 calmodulin dependent kinase signaling pathway; its suggested GO:0061762 CAMKK-AMPK signaling cascade does not involve CaMKII. No CaMKII-specific process term exists. - subject_id: PW:0000542 subject_label: adenosine monophosphate-activated protein kinase (AMPK) signaling pathway predicate_id: skos:narrowMatch object_id: GO:0061762 object_label: CAMKK-AMPK signaling cascade mapping_justification: semapv:ManualMappingCuration comment: >- GO:0061762 covers activation of AMPK by CAMKK only; the PW pathway also includes the LKB1 route (CAB39) and AMPK's downstream effects on mTORC1. GO has no general AMPK signalling term. - subject_id: PW:0001503 subject_label: auditory mechanotransduction pathway predicate_id: skos:narrowMatch object_id: GO:0050910 object_label: detection of mechanical stimulus involved in sensory perception of sound mapping_justification: semapv:ManualMappingCuration comment: The PW pathway covers vestibular as well as cochlear hair-cell mechanotransduction. - subject_id: PW:0000360 subject_label: hypoxia inducible factor pathway predicate_id: skos:narrowMatch object_id: GO:0097411 object_label: hypoxia-inducible factor-1alpha signaling pathway mapping_justification: semapv:ManualMappingCuration comment: GO:0097411 is HIF-1alpha only; the PW pathway also includes HIF-2alpha (EPAS1). - subject_id: PW:0000360 subject_label: hypoxia inducible factor pathway predicate_id: skos:broadMatch object_id: GO:0071456 object_label: cellular response to hypoxia mapping_justification: semapv:ManualMappingCuration - subject_id: PW:0000491 subject_label: vasopressin signaling pathway predicate_id: skos:closeMatch object_id: GO:1904117 object_label: cellular response to vasopressin mapping_justification: semapv:ManualMappingCuration comment: >- GO has no vasopressin receptor signaling pathway term; it uses the cellular-response term for the ligand. The pathway spans V1 (Gq) and V2 (Gs) receptors. - subject_id: PW:0000527 subject_label: angiotensin II signaling pathway via AT1 receptor predicate_id: skos:closeMatch object_id: GO:0086097 object_label: phospholipase C-activating angiotensin-activated signaling pathway mapping_justification: semapv:ManualMappingCuration comment: AT1 (AGTR1) couples to Gq/11 and phospholipase C. - subject_id: PW:0002635 subject_label: mitochondrial iron-sulfur cluster protein biogenesis pathway predicate_id: skos:broadMatch object_id: GO:0016226 object_label: iron-sulfur cluster assembly mapping_justification: semapv:ManualMappingCuration comment: >- GO has no mitochondrial-specific iron-sulfur cluster assembly term; GO:0097428 protein maturation by iron-sulfur cluster transfer is obsolete. - subject_id: PW:0000713 subject_label: vasopressin signaling pathway via receptor type 2 predicate_id: skos:broadMatch object_id: GO:0007189 object_label: adenylate cyclase-activating G protein-coupled receptor signaling pathway mapping_justification: semapv:ManualMappingCuration comment: >- GO has no vasopressin receptor signaling pathway term. GO:1904117 cellular response to vasopressin also covers V1 receptors, so the V2 branch maps only to its coupling term; AVPR2 couples to Gs. - subject_id: PW:0000713 subject_label: vasopressin signaling pathway via receptor type 2 predicate_id: skos:broadMatch object_id: GO:1904117 object_label: cellular response to vasopressin mapping_justification: semapv:ManualMappingCuration comment: The V2 receptor branch is one part of the cellular response to vasopressin. - subject_id: PW:0000493 subject_label: corticotropin-releasing hormone signaling pathway predicate_id: skos:closeMatch object_id: GO:0071376 object_label: cellular response to corticotropin-releasing hormone stimulus mapping_justification: semapv:ManualMappingCuration comment: >- GO has no CRH receptor signaling pathway term; it uses the cellular-response term for the ligand. CRHR1 and CRHR2 couple to Gs. - subject_id: PW:0000528 subject_label: angiotensin II signaling pathway via AT2 receptor predicate_id: skos:broadMatch object_id: GO:0038166 object_label: angiotensin-activated signaling pathway mapping_justification: semapv:ManualMappingCuration comment: >- GO has no AT2-specific term; AT2 does not signal through phospholipase C. GO:1904385 cellular response to angiotensin is broader still. - subject_id: PW:0001141 subject_label: calcium signaling pathway via the calcium-sensing receptor predicate_id: skos:broadMatch object_id: GO:0007186 object_label: G protein-coupled receptor signaling pathway mapping_justification: semapv:ManualMappingCuration comment: >- GO has no calcium-sensing receptor signaling pathway term. The cellular-response branch has only GO:0071277 cellular response to calcium ion, which covers every calcium response, not one receptor's. CASR couples to Gq/11 and Gi/o. - subject_id: PW:0002636 subject_label: cytosolic iron-sulfur cluster protein assembly pathway predicate_id: skos:broadMatch object_id: GO:0016226 object_label: iron-sulfur cluster assembly mapping_justification: semapv:ManualMappingCuration comment: GO has no term for cytosolic (CIA) iron-sulfur cluster assembly. - subject_id: PW:0000794 subject_label: epinephrine signaling pathway via adrenergic receptor beta predicate_id: skos:closeMatch object_id: GO:0071880 object_label: adenylate cyclase-activating adrenergic receptor signaling pathway mapping_justification: semapv:ManualMappingCuration comment: Beta adrenergic receptors couple to Gs; PW notes beta-2 can also couple to Gi. - subject_id: PW:0001135 subject_label: parathyroid hormone signaling pathway predicate_id: skos:closeMatch object_id: GO:0071374 object_label: cellular response to parathyroid hormone stimulus mapping_justification: semapv:ManualMappingCuration comment: >- GO has no PTH receptor signaling pathway term; it uses the cellular-response term for the ligand. PTH1R couples to Gs and Gq/11. - subject_id: PW:0001437 subject_label: titanium dioxide nanoparticle response pathway predicate_id: skos:broadMatch object_id: GO:1990267 object_label: response to transition metal nanoparticle mapping_justification: semapv:ManualMappingCuration comment: GO has no titanium-specific nanoparticle response term. - subject_id: PW:0001480 subject_label: kinin signaling pathway predicate_id: skos:broadMatch object_id: GO:0007186 object_label: G protein-coupled receptor signaling pathway mapping_justification: semapv:ManualMappingCuration comment: >- GO has no bradykinin receptor signaling pathway term, although GO:0140162 venom-mediated vasodilation by activation of bradykinin receptor signaling pathway names one, and no response-to-bradykinin term either. GO:0002254 kinin cascade and its children are the generation of kinins, not their signalling. BDKRB1 and BDKRB2 couple mainly to Gq/11. - subject_id: PW:0000676 subject_label: glucagon signaling pathway predicate_id: skos:closeMatch object_id: GO:0071377 object_label: cellular response to glucagon stimulus mapping_justification: semapv:ManualMappingCuration comment: >- GO has no glucagon receptor signaling pathway term; it uses the cellular-response term for the ligand, which is also the process of the mouse GO-CAM 636d9ce800000147. GCGR couples to Gs.