# GENERATED FILE - do not edit by hand. # Source of truth: the sibling *.sssom.yaml # Regenerate: uv run python projects/TCDB/sssom_to_terms.py .sssom.yaml -o .terms.yaml # Validate: uv run linkml-term-validator validate-data .terms.yaml -s src/ai_gene_review/schema/tcdb_go_mapping.yaml -t TCDBGOMappingSet --labels -c conf/oak_config.yaml mappings: - subject: id: TC:2.A.69 label: The Auxin Efflux Carrier (AEC) Family predicate: id: skos:exactMatch label: exact match object: id: GO:0010329 label: auxin efflux transmembrane transporter activity mapping_justification: semapv:ManualMappingCuration comment: 'Propagation: JUSTIFIED at family level. The AEC family (PIN proteins) is mono-specific for auxin efflux, so any 2.A.69 member can inherit GO:0010329. Backed by Arabidopsis PIN1 (Q9C6B8, DR TCDB 2.A.69.1.1) reviewed in this repo with GO:0010329 by IDA and IMP. Not a GO xref; not in any external2go mapping.' - subject: id: TC:2.A.22.1.1 label: The Neurotransmitter:Sodium Symporter (NSS) Family predicate: id: skos:exactMatch label: exact match object: id: GO:0005335 label: serotonin:sodium:chloride symporter activity mapping_justification: semapv:ManualMappingCuration comment: 'Propagation: JUSTIFIED at system level. TC 2.A.22.1.1 is specifically the serotonin transporter (SERT), so this 5-level id maps cleanly to GO:0005335. Backed by human SERT/SLC6A4 (P31645), which carries GO:0005335 (verified live). Curated up from a GO source: GO already xrefs this TC on GO:0005335 (also GO-xref''d), and here the propagation is confirmed justifiable. Note the parent FAMILY 2.A.22 (NSS) is poly-specific (dopamine, GABA, glycine, ...), so only the 5-level id propagates -- not the family.' - subject: id: TC:3.A.3.1.1 label: The P-type ATPase (P-ATPase) Superfamily predicate: id: skos:exactMatch label: exact match object: id: GO:0005391 label: P-type sodium:potassium-exchanging transporter activity mapping_justification: semapv:ManualMappingCuration comment: 'Propagation: JUSTIFIED at system level. TC 3.A.3.1.1 is the Na+/K+-exchanging P-type ATPase, so this 5-level id maps cleanly to GO:0005391. Backed by human ATP1A1 (P05023, EC 7.2.2.13) which carries GO:0005391 (verified live). Curated up from a GO source (also GO-xref''d). The P-ATPase superfamily 3.A.3 as a whole pumps many cations (H+, Ca2+, Cu+, ...), so only the 5-level id propagates.' - subject: id: TC:1.A.8 label: The Major Intrinsic Protein (MIP) Family predicate: id: skos:narrowMatch label: narrow match object: id: GO:0015250 label: water channel activity mapping_justification: semapv:ManualMappingCuration comment: 'Propagation: NOT justified at family level. The MIP family splits into classical aquaporins (water) and aquaglyceroporins (glycerol), so a 1.A.8 member cannot be assumed to be a water channel -- propagate only to the aquaporin subfamily. Backed by human AQP1 (P29972, DR TCDB 1.A.8.8.1, GO:0015250, verified live) for the water-channel subfamily specifically. Not a GO xref; not in any external2go mapping.' - subject: id: TC:2.A.17 label: The Proton-dependent Oligopeptide Transporter (POT/PTR) Family predicate: id: skos:narrowMatch label: narrow match object: id: GO:0015112 label: nitrate transmembrane transporter activity mapping_justification: semapv:ManualMappingCuration comment: 'Propagation: NOT justified at family level (worked case). The POT/PTR family is broadly a proton-dependent oligopeptide transporter; only the plant NRT1/NPF subfamily transports nitrate, so GO:0015112 must not propagate to the whole family. Backed by Arabidopsis CHL1/NRT1.1 (Q05085, DR TCDB 2.A.17.3.1) reviewed in this repo with GO:0015112 by IMP (also GO-xref''d).' - subject: id: TC:2.A.18 label: The Amino Acid/Auxin Permease (AAAP) Family predicate: id: skos:narrowMatch label: narrow match object: id: GO:0010328 label: auxin influx transmembrane transporter activity mapping_justification: semapv:ManualMappingCuration comment: 'Propagation: NOT justified at family level. The AAAP family is broadly an amino acid permease (family-level term GO:0015171); only the AUX/LAX subfamily is a proton-driven auxin importer, so GO:0010328 propagates to that subfamily only. Backed by Arabidopsis AUX1 (Q96247, DR TCDB 2.A.18.1.1) reviewed in this repo with GO:0010328 by IDA (also GO-xref''d).' - subject: id: TC:2.A.36 label: The Monovalent Cation:Proton Antiporter-1 (CPA1) Family predicate: id: skos:narrowMatch label: narrow match object: id: GO:0015385 label: sodium:proton antiporter activity mapping_justification: semapv:ManualMappingCuration comment: 'Propagation: NOT justified at family level. The CPA1 family is monovalent-cation:proton antiporters; the exact cation (Na+, K+) is member-specific, so GO:0015385 is a subfamily property (family-level term is GO:0015297 antiporter activity). Backed by Arabidopsis SOS1 (Q9LKW9, DR TCDB 2.A.36.7.6) reviewed in this repo, a plasma-membrane Na+/H+ antiporter (also GO-xref''d).' - subject: id: TC:2.A.38 label: The K+ Transporter (Trk) Family predicate: id: skos:narrowMatch label: narrow match object: id: GO:0015079 label: potassium ion transmembrane transporter activity mapping_justification: semapv:ManualMappingCuration comment: 'Propagation: NOT justified at family level. The Trk/Ktr/HKT family is broadly a K+ transporter, but the plant HKT subfamily includes Na+-selective members, so substrate is subfamily-dependent. Backed by yeast TRK1 (P12685, DR TCDB 2.A.38.2.1), which carries GO:0015079 by IDA (SGD) -- the K+ activity is real for the Trk subfamily. The COUNTER-EXAMPLE that makes this narrowMatch rather than exactMatch is Arabidopsis HKT1 (Q84TI7, DR TCDB 2.A.38.3.2), reviewed in this repo: its GO:0015079 is IEA and is marked MARK_AS_OVER_ANNOTATED (AtHKT1;1 is Na+-selective, lacks the conserved Gly-68 of K+-permeable HKTs, and does not transport K+ in planta; its experimentally supported activity is GO:0015081 Na+ by IDA). Propagating GO:0015079 across 2.A.38 would reproduce exactly that over-annotation. GO xrefs the family, but to GO:0015387 / GO:0009674, not to GO:0015079.'