# GENERATED FILE - do not edit by hand. # Source of truth: projects/NCBIFam/ncbifam2go.sssom.yaml # Regenerate: uv run python projects/NCBIFam/sssom_to_terms.py projects/NCBIFam/ncbifam2go.sssom.yaml -o projects/NCBIFam/ncbifam2go.terms.yaml # Validate: uv run linkml-term-validator validate-data projects/NCBIFam/ncbifam2go.terms.yaml -s src/ai_gene_review/schema/ncbifam_go_mapping.yaml -t NCBIFAMGOMappingSet --labels -c conf/oak_config.yaml mappings: - subject: id: NCBIFAM:NF009803 label: formamidase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0004328 label: formamidase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge supported: hmm_PGAP gives EC 3.5.1.49 and ec2go maps EC 3.5.1.49 -> exactly GO:0004328. equivalog family. Propagation gain: gain_rev=0 (27/27 reviewed already have it) but gain_all=54 -- the gap is entirely in unreviewed TrEMBL entries carrying NF009803.' - subject: id: NCBIFAM:NF005824 label: acetolactate synthase large subunit (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0003984 label: acetolactate synthase activity mapping_justification: semapv:ManualMappingCuration comment: The large (catalytic) subunit carries the activity. equivalog. gain_rev=0 (1/1), gain_all=6. Clean propagation case -- nearly fully covered already, included as an exactMatch exemplar. - subject: id: NCBIFAM:NF045700 label: AttM family quorum-quenching N-acyl homoserine lactonase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0102007 label: acyl-L-homoserine-lactone lactonohydrolase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge supported: EC 3.1.1.81 -> GO:0102007 in ec2go. equivalog, PMID:11930013. Quorum quenching. gain_rev=0 (4/4), gain_all=115 -- large TrEMBL gap.' - subject: id: NCBIFAM:TIGR03230 label: lipoprotein lipase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0004465 label: lipoprotein lipase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge supported: EC 3.1.1.34 -> GO:0004465 in ec2go. equivalog, PMID:8308035. gain_rev=0 (11/11), gain_all=9.' - subject: id: NCBIFAM:NF033545 label: IS630 family transposase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0004803 label: transposase activity mapping_justification: semapv:ManualMappingCuration comment: 'equivalog. The single largest propagation gap in the scoping sample: gain_all=18874 of 18881 entries carrying NF033545 lack GO:0004803 (or any descendant), and gain_rev=2. Mobile-element families are precisely where InterPro integration lags, so NCBIFAM''s GO is unused.' - subject: id: NCBIFAM:NF041162 label: family 2A encapsulin nanocompartment shell protein (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0140737 label: encapsulin nanocompartment mapping_justification: semapv:ManualMappingCuration comment: 'Cellular-component mapping: the shell protein localises to / constitutes the encapsulin nanocompartment. equivalog, PMID:25024436,34362927,35146412. gain_all=897 of 901, gain_rev=0.' - subject: id: NCBIFAM:NF042963 label: anti-phage-associated DUF1156 domain-containing protein (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0051607 label: defense response to virus mapping_justification: semapv:ManualMappingCuration comment: Biological-process mapping for an anti-phage defense family. equivalog, PMID:32855333. gain_all=151 of 151 (0 carry the term), gain_rev=0 -- a brand-new defense family with no GO propagation at all; a clear gap-fill / proposed-annotation candidate. - subject: id: NCBIFAM:NF000320 label: PEN family class A beta-lactamase, Bcc-type (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0008800 label: beta-lactamase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 3.5.2.6 -> GO:0008800 in ec2go. AMR-relevant. equivalog, PMID:19075063,9371340. gain_all=0 of 45 (already fully covered in this reviewed-heavy family), included as a clean AMR exemplar; cf. NF033105 (a different beta-lactamase family) which maps to the same GO term.' - subject: id: NCBIFAM:NF033105 label: subclass B3 metallo-beta-lactamase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0008800 label: beta-lactamase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 3.5.2.6 -> GO:0008800. AMR-relevant (carbapenem-hydrolysing metallo class). equivalog. gain_all=165 of 1170 -- a substantial TrEMBL gap. Two distinct NCBIFAM families (NF000320 serine class A, NF033105 metallo B3) legitimately share one GO term: family -> GO is many-to-one, the structural analog of RHEA''s many-reactions-to-one-activity finding.' - subject: id: NCBIFAM:NF002525 label: D-alanine--D-alanine ligase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0008716 label: D-alanine-D-alanine ligase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 6.3.2.4 -> GO:0008716. Peptidoglycan biosynthesis (Ddl, a vancomycin-resistance locus). equivalog. gain_all=3 of 777, gain_rev=0.' - subject: id: NCBIFAM:NF003009 label: 5'-deoxynucleotidase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0002953 label: 5'-deoxynucleotidase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 3.1.3.89 -> GO:0002953. equivalog. gain_all=170 of 1714, gain_rev=0.' - subject: id: NCBIFAM:NF004018 label: uridine kinase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0004849 label: uridine kinase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 2.7.1.48 -> GO:0004849. Pyrimidine salvage. equivalog. gain_all=329 of 15080 -- the largest TrEMBL gap among the enzyme rows in this batch; gain_rev=0.' - subject: id: NCBIFAM:NF006707 label: class I fructose-bisphosphate aldolase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0004332 label: fructose-bisphosphate aldolase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 4.1.2.13 -> GO:0004332. Glycolysis. equivalog. gain_all=4 of 1476, gain_rev=0.' - subject: id: NCBIFAM:NF007054 label: alpha-amylase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0004556 label: alpha-amylase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 3.2.1.1 -> GO:0004556. equivalog. gain_all=1 of 37, gain_rev=0.' - subject: id: NCBIFAM:NF011000 label: acylphosphatase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0003998 label: acylphosphatase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 3.6.1.7 -> GO:0003998. equivalog. gain_all=4 of 1135, gain_rev=0.' - subject: id: NCBIFAM:NF040791 label: glycerate 2-kinase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0043798 label: glycerate 2-kinase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 2.7.1.165 -> GO:0043798. equivalog, PMID:16684110. gain_all=6 of 7 -- small but nearly total gap for this family.' - subject: id: NCBIFAM:NF045654 label: acid phosphatase PhoC (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0003993 label: acid phosphatase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 3.1.3.2 -> GO:0003993. equivalog, PMID:10877772,8081499. gain_all=1 of 80.' - subject: id: NCBIFAM:TIGR02321 label: phosphonopyruvate hydrolase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0033978 label: phosphonopyruvate hydrolase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 3.11.1.3 -> GO:0033978. Phosphonate catabolism. equivalog, PMID:12697754. gain_all=71 of 137, gain_rev=0.' - subject: id: NCBIFAM:TIGR02694 label: arsenate reductase (azurin) small subunit (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0050611 label: arsenate reductase (azurin) activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 1.20.9.1 -> GO:0050611. Arsenic detoxification/respiration. equivalog, PMID:12679550. gain_all=144 of 355, and gain_rev=2 -- reviewed entries are missing it too.' - subject: id: NCBIFAM:TIGR03828 label: 1-phosphofructokinase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0008662 label: 1-phosphofructokinase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 2.7.1.56 -> GO:0008662. Fructose catabolism. equivalog. gain_all=16 of 5974, gain_rev=0.' - subject: id: NCBIFAM:NF001277 label: adenosylcobinamide-GDP ribazoletransferase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0051073 label: adenosylcobinamide-GDP ribazoletransferase activity mapping_justification: semapv:ManualMappingCuration comment: 'EC-bridge: EC 2.7.8.26 -> GO:0051073. Cobalamin (B12) biosynthesis (CobS). equivalog. gain_all=4 of 1293, gain_rev=0.' - subject: id: NCBIFAM:NF002326 label: deoxyguanosinetriphosphate triphosphohydrolase / dGTPase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0008832 label: dGTPase activity mapping_justification: semapv:ManualMappingCuration comment: Our proposed term. NCBI's go_terms gave only the broad parent GO:0016793 (triphosphoric monoester hydrolase activity); the specific GO:0008832 (dGTPase activity) is correct (product name = dGTPase, EC 3.1.5.1; ec2go EC 3.1.5.1 -> GO:0008832). equivalog. Against the specific term gain_all=456 of 3719 and gain_rev=13 -- a substantial reviewed gap the broad parent (gain~0) hid entirely. - subject: id: NCBIFAM:NF005804 label: enoyl-CoA hydratase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0004300 label: enoyl-CoA hydratase activity mapping_justification: semapv:ManualMappingCuration comment: Our proposed term. NCBI assigned the ontology near-root GO:0003824 (catalytic activity) to this EC 4.2.1.17 enzyme; ec2go maps EC 4.2.1.17 -> GO:0004300 directly. equivalog. Against the specific term gain_all=184 of 485, gain_rev=1 (the GO:0003824 parent gain was ~0 -- altitude masking). - subject: id: NCBIFAM:NF006559 label: dihydroorotase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0004151 label: dihydroorotase activity mapping_justification: semapv:ManualMappingCuration comment: Our proposed term. NCBI assigned the broad parent GO:0016810; the specific GO:0004151 is the ec2go target of EC 3.5.2.3. Pyrimidine biosynthesis (PyrC). equivalog. Against the specific term gain_all=491 of 1354 (vs 4 for the broad parent), gain_rev=0. - subject: id: NCBIFAM:TIGR00417 label: spermidine synthase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0004766 label: spermidine synthase activity mapping_justification: semapv:ManualMappingCuration comment: Our proposed term. NCBI assigned the ontology near-root GO:0003824 (catalytic activity) to this EC 2.5.1.16 enzyme; ec2go maps EC 2.5.1.16 -> GO:0004766 directly. Polyamine biosynthesis. equivalog. Against the specific term gain_all=575 of 9260 and gain_rev=1 (the GO:0003824 parent gain was ~0). - subject: id: NCBIFAM:TIGR03542 label: LL-diaminopimelate aminotransferase (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0010285 label: L,L-diaminopimelate:2-oxoglutarate transaminase activity mapping_justification: semapv:ManualMappingCuration comment: Our proposed term. NCBI assigned the broad class GO:0008483 (transaminase activity); the specific GO:0010285 is the ec2go target of EC 2.6.1.83. Lysine/peptidoglycan biosynthesis. equivalog, PMID:17093042,17583737. Against the specific term gain_all=1185 of 2649 (vs 77 for the broad class), gain_rev=2. - subject: id: NCBIFAM:TIGR02791 label: P-type DNA transfer protein VirB5 (equivalog) predicate: id: skos:broadMatch label: broad match object: id: GO:0043684 label: type IV secretion system complex mapping_justification: semapv:ManualMappingCuration comment: VirB5 is a minor pilus/component subunit part_of the T4SS; the GO term is the whole complex, so the relation is part_of (broadMatch), not exact, and there is no VirB5-specific CC term to propose. equivalog, PMID:12855161,14673074,15901731. gain_all=298 of 298 (0 carry it), gain_rev=4. - subject: id: NCBIFAM:TIGR00439 label: permease-like cell division protein FtsX (equivalog) predicate: id: skos:exactMatch label: exact match object: id: GO:0051301 label: cell division mapping_justification: semapv:ManualMappingCuration comment: 'Our proposed term, chosen against NCBI''s GO:0000910 (cytokinesis) on empirical + ontology grounds. Ontology: GO:0000910 cytokinesis is part_of GO:0051301 cell division, so NCBI''s term is actually NARROWER, not broader. Empirically all 7 reviewed FtsX proteins carry GO:0051301 (cell division) but only 2/7 carry cytokinesis or GO:0043093 (FtsZ-dependent cytokinesis). FtsX/FtsEX regulates septal peptidoglycan hydrolysis and divisome assembly, so the conservative participation term (cell division) is the curator consensus. gain_all=22 of 3306 (already near-universal -- a confirmatory, low-gap mapping). NOTE: mapping to the specific GO:0043093 instead would show a huge apparent gain (3304) but curators apply it to only 2/7 entries, so blanket propagation would be OVER-ANNOTATION -- we deliberately keep the safe consensus term. The opposite call from the five altitude rows above, where the specific term WAS the correct, universally-applicable one.'