mycobase_sqlite_seed_data.sql

-- ===================================================================
-- MycoBase seed data
-- Synthetic but realistic rows for stress-testing text-to-SQL.
-- ===================================================================
BEGIN TRANSACTION;

-- sys_users
INSERT INTO sys_users (id, uuid, username, email, display_name, is_active, is_curator) VALUES
  (1, '11111111-1111-1111-1111-111111111111', 'egc', 'egc@bot.example.org', 'Elsie G. Curtis', 1, 1),
  (2, '22222222-2222-2222-2222-222222222222', 'rkato', 'rkato@myco.example.jp', 'Ryo Kato', 1, 1),
  (3, '33333333-3333-3333-3333-333333333333', 'mlind', 'm.lindberg@gen.example.se', 'Märta Lindberg', 1, 0),
  (4, '44444444-4444-4444-4444-444444444444', 'asankar', 'a.sankaranarayanan@iisc.example.in', 'Anjali Sankaranarayanan', 1, 1);



-- geo_continents
INSERT INTO geo_continents (id, code, label, display_order, is_active) VALUES
  (1, 'EU', 'Europe', 1, 1),
  (2, 'NA', 'North America', 2, 1),
  (3, 'SA', 'South America', 3, 1),
  (4, 'AS', 'Asia', 4, 1),
  (5, 'AF', 'Africa', 5, 1),
  (6, 'OC', 'Oceania', 6, 1),
  (7, 'AN', 'Antarctica', 7, 1);



-- geo_countries
INSERT INTO geo_countries (id, iso_alpha2, iso_alpha3, iso_numeric, name, continent_id) VALUES
  (1, 'PL', 'POL', 616, 'Poland', 1),
  (2, 'US', 'USA', 840, 'United States', 2),
  (3, 'JP', 'JPN', 392, 'Japan', 4),
  (4, 'BR', 'BRA', 76, 'Brazil', 3),
  (5, 'SE', 'SWE', 752, 'Sweden', 1),
  (6, 'IN', 'IND', 356, 'India', 4),
  (7, 'DE', 'DEU', 276, 'Germany', 1),
  (8, 'GB', 'GBR', 826, 'United Kingdom', 1),
  (9, 'AU', 'AUS', 36, 'Australia', 6),
  (10, 'CN', 'CHN', 156, 'China', 4);



-- geo_biomes
INSERT INTO geo_biomes (id, code, label, display_order, is_active, typical_temperature_c, typical_precipitation_mm) VALUES
  (1, 'TBMF', 'Temperate broadleaf & mixed forest', 1, 1, 10.0, 900),
  (2, 'TCF', 'Temperate coniferous forest', 2, 1, 6.0, 1200),
  (3, 'TRF', 'Tropical & subtropical moist broadleaf forest', 3, 1, 24.0, 2200),
  (4, 'BORF', 'Boreal forest / taiga', 4, 1, -1.0, 500),
  (5, 'MOMG', 'Montane grassland & shrubland', 5, 1, 8.0, 700);



-- geo_localities
INSERT INTO geo_localities (id, uuid, name, country_id, decimal_latitude, decimal_longitude, elevation_m) VALUES
  (1, 'aaaa1111-1111-1111-1111-111111111111', 'Białowieża Forest, oak-hornbeam stand BPN-A3', 1, 52.7, 23.87, 165),
  (2, 'aaaa2222-2222-2222-2222-222222222222', 'Mt. Hood National Forest, Oregon, Cascade conifer slope', 2, 45.37, -121.69, 1340),
  (3, 'aaaa3333-3333-3333-3333-333333333333', 'Yakushima island, evergreen broadleaf forest near Shiratani', 3, 30.32, 130.55, 620),
  (4, 'aaaa4444-4444-4444-4444-444444444444', 'Atlantic Forest fragment, Serra do Mar, Cubatão', 4, -23.86, -46.42, 380),
  (5, 'aaaa5555-5555-5555-5555-555555555555', 'Abisko subarctic taiga, birch–pine ecotone', 5, 68.36, 18.78, 410);



-- people_institutions
INSERT INTO people_institutions (id, name, acronym, country_id) VALUES
  (1, 'Royal Botanic Gardens, Kew', 'RBG-K', 8),
  (2, 'New York Botanical Garden', 'NYBG', 2),
  (3, 'Naturalis Biodiversity Center', 'NL', 7),
  (4, 'Indian Institute of Science', 'IISc', 6),
  (5, 'Polish Academy of Sciences, Białowieża Geobotanical Station', 'PAS-BIA', 1);



-- people_herbaria
INSERT INTO people_herbaria (id, institution_id, ih_code, name, specimen_count_estimate) VALUES
  (1, 1, 'K', 'Kew Mycology Herbarium', 1250000),
  (2, 2, 'NY', 'NYBG William and Lynda Steere Herbarium', 8000000),
  (3, 3, 'L', 'Naturalis Cryptogamic Herbarium', 2000000);



-- people_persons
INSERT INTO people_persons (id, uuid, family_name, given_names, standard_form, is_collector, is_taxonomist) VALUES
  (1, 'bbbb1111-1111-1111-1111-111111111111', 'Persoon', 'Christiaan Hendrik', 'Pers.', 0, 1),
  (2, 'bbbb2222-2222-2222-2222-222222222222', 'Fries', 'Elias Magnus', 'Fr.', 0, 1),
  (3, 'bbbb3333-3333-3333-3333-333333333333', 'Kalichman', 'Joshua', 'Kalichman', 1, 1),
  (4, 'bbbb4444-4444-4444-4444-444444444444', 'Ohenoja', 'Esteri', 'Ohenoja', 1, 1),
  (5, 'bbbb5555-5555-5555-5555-555555555555', 'Singer', 'Rolf', 'Singer', 0, 1);



-- lit_publication_types
INSERT INTO lit_publication_types (id, code, label, display_order, is_active) VALUES
  (1, 'JART', 'Journal article', 1, 1),
  (2, 'BOOK', 'Book', 2, 1),
  (3, 'MONO', 'Monograph', 3, 1),
  (4, 'THES', 'Thesis', 4, 1);



-- lit_journals
INSERT INTO lit_journals (id, title, abbreviation, issn_online, publisher) VALUES
  (1, 'Mycologia', 'Mycologia', '1557-2536', 'Mycological Society of America'),
  (2, 'Persoonia', 'Persoonia', '1878-9080', 'Naturalis'),
  (3, 'Fungal Diversity', 'Fungal Divers.', '1878-9129', 'Springer Nature');



-- lit_publications
INSERT INTO lit_publications (id, uuid, publication_type_id, title, year, journal_id, volume, page_start, page_end, doi) VALUES
  (1, 'cccc1111-1111-1111-1111-111111111111', 1, 'Phylogenetic placement of Galerina marginata: a re-evaluation', 2021, 1, '113', '204', '221', '10.1080/00275514.2021.0001'),
  (2, 'cccc2222-2222-2222-2222-222222222222', 1, 'Boletus edulis sensu lato: cryptic diversity in Eurasia', 2019, 2, '43', '1', '32', '10.3767/persoonia.2019.43.01'),
  (3, 'cccc3333-3333-3333-3333-333333333333', 3, 'Monograph of Russula in the Pacific Northwest', 2017, NULL, NULL, NULL, NULL, NULL);



-- tax_nomenclatural_codes
INSERT INTO tax_nomenclatural_codes (id, code, label, display_order, is_active) VALUES
  (1, 'ICNAFP', 'International Code of Nomenclature for algae, fungi, and plants', 1, 1);



-- tax_taxonomic_status
INSERT INTO tax_taxonomic_status (id, code, label, display_order, is_active) VALUES
  (1, 'ACCEPTED', 'Accepted', 1, 1),
  (2, 'SYNONYM', 'Synonym', 2, 1),
  (3, 'DOUBTFUL', 'Doubtful (nomen dubium)', 3, 1),
  (4, 'MISAPPLIED', 'Misapplied name', 4, 1);



-- tax_kingdoms
INSERT INTO tax_kingdoms (id, uuid, scientific_name, authority, year_published, nomenclatural_code_id, status_id) VALUES
  (1, 'dddd0001-0001-0001-0001-000000000001', 'Fungi', 'Bartling', 1830, 1, 1);



-- tax_phyla
INSERT INTO tax_phyla (id, uuid, scientific_name, authority, nomenclatural_code_id, status_id, parent_subkingdom_id) VALUES
  (1, 'dddd0002-0001-0001-0001-000000000001', 'Basidiomycota', 'R.T. Moore', 1, 1, NULL),
  (2, 'dddd0002-0001-0001-0001-000000000002', 'Ascomycota', 'Caval.-Sm.', 1, 1, NULL);



-- tax_classes
INSERT INTO tax_classes (id, uuid, scientific_name, authority, nomenclatural_code_id, status_id) VALUES
  (1, 'dddd0003-0001-0001-0001-000000000001', 'Agaricomycetes', 'Doweld', 1, 1),
  (2, 'dddd0003-0001-0001-0001-000000000002', 'Sordariomycetes', 'O.E. Erikss. & Winka', 1, 1);



-- tax_orders
INSERT INTO tax_orders (id, uuid, scientific_name, authority, nomenclatural_code_id, status_id) VALUES
  (1, 'dddd0004-0001-0001-0001-000000000001', 'Agaricales', 'Underw.', 1, 1),
  (2, 'dddd0004-0001-0001-0001-000000000002', 'Boletales', 'E.-J. Gilbert', 1, 1),
  (3, 'dddd0004-0001-0001-0001-000000000003', 'Russulales', 'Kreisel ex P.M. Kirk, P.F. Cannon & J.C. David', 1, 1),
  (4, 'dddd0004-0001-0001-0001-000000000004', 'Hypocreales', 'Lindau', 1, 1);



-- tax_families
INSERT INTO tax_families (id, uuid, scientific_name, authority, nomenclatural_code_id, status_id, is_type_genus) VALUES
  (1, 'dddd0005-0001-0001-0001-000000000001', 'Amanitaceae', 'E.-J. Gilbert', 1, 1, 0),
  (2, 'dddd0005-0001-0001-0001-000000000002', 'Boletaceae', 'Chevall.', 1, 1, 0),
  (3, 'dddd0005-0001-0001-0001-000000000003', 'Russulaceae', 'Lotsy', 1, 1, 0),
  (4, 'dddd0005-0001-0001-0001-000000000004', 'Strophariaceae', 'Singer & A.H. Sm.', 1, 1, 0);



-- tax_genera
INSERT INTO tax_genera (id, uuid, scientific_name, authority, nomenclatural_code_id, status_id) VALUES
  (1, 'dddd0006-0001-0001-0001-000000000001', 'Amanita', 'Pers.', 1, 1),
  (2, 'dddd0006-0001-0001-0001-000000000002', 'Boletus', 'L.', 1, 1),
  (3, 'dddd0006-0001-0001-0001-000000000003', 'Russula', 'Pers.', 1, 1),
  (4, 'dddd0006-0001-0001-0001-000000000004', 'Galerina', 'Earle', 1, 1),
  (5, 'dddd0006-0001-0001-0001-000000000005', 'Ophiocordyceps', 'Petch', 1, 1);



-- tax_species
INSERT INTO tax_species (id, uuid, scientific_name, authority, year_published, nomenclatural_code_id, status_id, mycobank_number) VALUES
  (1, 'dddd0007-0001-0001-0001-000000000001', 'Amanita phalloides', '(Vaill. ex Fr.) Link', 1833, 1, 1, 121343),
  (2, 'dddd0007-0001-0001-0001-000000000002', 'Boletus edulis', 'Bull.', 1782, 1, 1, 198611),
  (3, 'dddd0007-0001-0001-0001-000000000003', 'Russula emetica', '(Schaeff.) Pers.', 1796, 1, 1, 200020),
  (4, 'dddd0007-0001-0001-0001-000000000004', 'Galerina marginata', '(Batsch) Kühner', 1935, 1, 1, 280003),
  (5, 'dddd0007-0001-0001-0001-000000000005', 'Ophiocordyceps sinensis', '(Berk.) G.H. Sung, J.M. Sung, Hywel-Jones & Spatafora', 2007, 1, 1, 511803),
  (6, 'dddd0007-0001-0001-0001-000000000006', 'Amanita muscaria', '(L.) Lam.', 1783, 1, 1, 100002);



-- spc_preservation_methods
INSERT INTO spc_preservation_methods (id, code, label, display_order, is_active) VALUES
  (1, 'DRIED', 'Dried', 1, 1),
  (2, 'ETOH', '70% ethanol', 2, 1),
  (3, 'FROZEN', 'Frozen at -80 C', 3, 1),
  (4, 'SILICA', 'Silica gel', 4, 1);



-- spc_collection_events
INSERT INTO spc_collection_events (id, uuid, event_date, locality_id, habitat_summary, temperature_c) VALUES
  (1, 'eeee0001-0001-0001-0001-000000000001', '2022-09-12', 1, 'Mature oak-hornbeam stand, mossy logs', 14.2),
  (2, 'eeee0002-0002-0002-0002-000000000002', '2021-10-04', 2, 'Douglas-fir canopy, deep litter on north slope', 9.5),
  (3, 'eeee0003-0003-0003-0003-000000000003', '2023-08-15', 3, 'Sphagnum moss carpet under Cryptomeria', 19.0);



-- spc_specimens
INSERT INTO spc_specimens (id, uuid, catalog_number, herbarium_id, collection_event_id, collector_number, primary_collector_person_id, preservation_method_id, identified_species_id, identified_at_rank, identification_confidence, is_type_specimen, condition_score) VALUES
  (1, 'ffff0001-0001-0001-0001-000000000001', 'K(M)281044', 1, 1, 'EGC-2022-103', 3, 1, 1, 'species', 'expert', 0, 5),
  (2, 'ffff0002-0002-0002-0002-000000000002', 'NY01234567', 2, 2, 'JK-217', 3, 1, 2, 'species', 'expert', 0, 4),
  (3, 'ffff0003-0003-0003-0003-000000000003', 'NY01234589', 2, 2, 'JK-218', 3, 1, 3, 'species', 'verified', 0, 4),
  (4, 'ffff0004-0004-0004-0004-000000000004', 'L0455123', 3, 3, 'RK-2023-08-15-04', 3, 1, 5, 'species', 'expert', 1, 5),
  (5, 'ffff0005-0005-0005-0005-000000000005', 'K(M)281099', 1, 1, 'EGC-2022-104', 3, 1, 4, 'species', 'tentative', 0, 3);



-- mor_chemical_reagents
INSERT INTO mor_chemical_reagents (id, code, label, display_order, is_active) VALUES
  (1, 'KOH3', '3% potassium hydroxide', 1, 1),
  (2, 'MELZ', 'Melzer''s reagent', 2, 1),
  (3, 'NH4OH', 'Ammonium hydroxide', 3, 1),
  (4, 'FESO4', 'Iron(II) sulfate', 4, 1);



-- mor_spore_measurements
INSERT INTO mor_spore_measurements (id, specimen_id, species_id, length_min_um, length_max_um, length_mean_um, width_min_um, width_max_um, width_mean_um, q_min, q_max, q_mean, sample_size_n, measured_in_reagent_id, excludes_apiculus) VALUES
  (1, 1, 1, 8.5, 11.0, 9.4, 7.0, 9.0, 8.1, 1.05, 1.3, 1.16, 30, 2, 1),
  (2, 2, 2, 13.0, 17.5, 15.2, 4.5, 6.0, 5.3, 2.55, 3.2, 2.87, 50, 1, 1),
  (3, 3, 3, 8.0, 11.0, 9.5, 7.0, 9.5, 8.2, 1.05, 1.25, 1.16, 25, 2, 1),
  (4, 4, 5, 10.0, 14.0, 12.0, 3.0, 4.0, 3.5, 3.0, 4.0, 3.4, 30, 1, 1);



-- bio_compound_classes
INSERT INTO bio_compound_classes (id, code, label, display_order, is_active) VALUES
  (1, 'ALK', 'Alkaloid', 1, 1),
  (2, 'PEPT', 'Peptide', 2, 1),
  (3, 'POLY', 'Polyketide', 3, 1),
  (4, 'TERP', 'Terpenoid', 4, 1);



-- bio_compounds
INSERT INTO bio_compounds (id, compound_class_id, preferred_name, molecular_formula, monoisotopic_mass_da, cas_number, is_secondary_metabolite) VALUES
  (1, 2, 'alpha-Amanitin', 'C39H54N10O14S', 918.3592, '23109-05-9', 1),
  (2, 2, 'beta-Amanitin', 'C39H53N9O15S', 919.3432, '21150-22-1', 1),
  (3, 2, 'Phalloidin', 'C35H48N8O11S', 788.3163, '17466-45-4', 1),
  (4, 1, 'Muscarine', 'C9H20NO2', 174.1494, '300-54-9', 1),
  (5, 1, 'Ibotenic acid', 'C5H6N2O4', 158.0327, '2552-55-8', 1),
  (6, 1, 'Psilocybin', 'C12H17N2O4P', 284.0926, '520-52-5', 1),
  (7, 4, 'Ergosterol', 'C28H44O', 396.3392, '57-87-4', 0);



-- bio_species_compound_occurrences
INSERT INTO bio_species_compound_occurrences (id, species_id, compound_id, specimen_id, concentration_mg_per_g, detection_method, publication_id) VALUES
  (1, 1, 1, 1, 0.45, 'HPLC-MS', 1),
  (2, 1, 2, 1, 0.29, 'HPLC-MS', 1),
  (3, 1, 3, 1, 0.082, 'HPLC-MS', 1),
  (4, 4, 1, 5, 0.041, 'HPLC-MS', 1),
  (5, 6, 5, NULL, 0.6, 'HPLC-UV', NULL),
  (6, 6, 6, NULL, 0.008, 'HPLC-UV', NULL);



-- bio_toxin_amatoxins
INSERT INTO bio_toxin_amatoxins (id, compound_id, ld50_mg_per_kg_mouse, primary_target_organ, symptom_onset_hours_min, symptom_onset_hours_max, publication_id) VALUES
  (1, 1, 0.1, 'liver', 6.0, 24.0, 1),
  (2, 2, 0.2, 'liver', 6.0, 24.0, 1);



-- gen_sequencing_platforms
INSERT INTO gen_sequencing_platforms (id, code, label, display_order, is_active) VALUES
  (1, 'ILL_NOV', 'Illumina NovaSeq 6000', 1, 1),
  (2, 'PB_SEQ', 'PacBio Sequel IIe', 2, 1),
  (3, 'ONT_PROM', 'Oxford Nanopore PromethION', 3, 1);



-- gen_sequences
INSERT INTO gen_sequences (id, uuid, specimen_id, dna_extract_id, library_id, locus, genbank_accession, sequence_md5, length_bp, gc_content_pct, sequence_text) VALUES
  (1, 'abcdef01-aaaa-bbbb-cccc-000000000001', 1, NULL, NULL, 'its', 'MZ000001', '63d713d7ab914cc1cfb701dbcaf17106', 126, 53.17, 'TCCGTAGGTGAACCTGCGGAAGGATCATTAACGAGTTACGCTGTGGAATGCAGCATTTAGCGGACTCAGTGCGGCAATCGTGTGGCCATCGGGCATTTGGGCAGGTCACAACTGAGTGAACAGTAC'),
  (2, 'abcdef02-aaaa-bbbb-cccc-000000000002', 2, NULL, NULL, 'its', 'MZ000002', 'daf2bc54d8c0d3c8211643874c81b9ef', 131, 45.8, 'TCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATTGTTTAGCAGTGGAGAACATGTAGAGCTGACTCAATGTGGCATCCATGCATGGCAATCACAGAGCAGTAACAACTAGGTAGAGCAACAGTGCATG'),
  (3, 'abcdef03-aaaa-bbbb-cccc-000000000003', 3, NULL, NULL, 'its', 'MZ000003', '1591f4316ba25767c7eab43e59ad4c0f', 132, 43.18, 'TCCGTAGGTGAACCTGCGGAAGGATCATTACAGTAGAACAGTTGCAATCATATGTGGCAACATGTAGCAGGAATCAACTAACGTGGCATTGTAGCAACAATGCATGCAGTAACATAGTAACTAATGGGCATG'),
  (4, 'abcdef04-aaaa-bbbb-cccc-000000000004', 5, NULL, NULL, 'its', 'MZ000004', '525588699097fee91c11eb88bdd11d73', 132, 42.42, 'TCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATGGTTTAGCAATGGCATATGTAGCATCACATTGCATGCATAGTAGAGCTAGCATGGCAACATCATGGCAAACAACAACATAGTAGCAACAATGCATG');



-- eco_iucn_assessments
INSERT INTO eco_iucn_assessments (id, species_id, assessment_year, category, rationale, publication_id) VALUES
  (1, 1, 2019, 'LC', 'Widespread in Europe and North America.', 1),
  (2, 2, 2019, 'LC', 'Common across the Holarctic.', 2),
  (3, 5, 2020, 'VU', 'Over-collection for traditional medicine; declining populations.', NULL);



-- eco_phenology_observations
INSERT INTO eco_phenology_observations (id, species_id, locality_id, observation_year, first_fruit_doy, peak_fruit_doy, last_fruit_doy) VALUES
  (1, 1, 1, 2022, 220, 256, 295),
  (2, 2, 2, 2021, 240, 275, 310),
  (3, 3, 1, 2022, 235, 268, 302),
  (4, 5, 3, 2023, 121, 145, 180);



-- pat_host_organism_kingdoms
INSERT INTO pat_host_organism_kingdoms (id, code, label, display_order, is_active) VALUES
  (1, 'PLANT', 'Plant', 1, 1),
  (2, 'AVERT', 'Animal (vertebrate)', 2, 1),
  (3, 'AINV', 'Animal (invertebrate)', 3, 1),
  (4, 'FUNG', 'Fungus', 4, 1);



-- pat_host_organisms
INSERT INTO pat_host_organisms (id, host_kingdom_id, host_family, host_genus, host_species, common_name) VALUES
  (1, 3, 'Hepialidae', 'Thitarodes', 'armoricanus', 'ghost moth larva'),
  (2, 1, 'Pinaceae', 'Pinus', 'sylvestris', 'Scots pine');



-- pat_diseases
INSERT INTO pat_diseases (id, code, label, display_order, is_active) VALUES
  (1, 'ENTPAR', 'Entomopathogenic infection (fungal)', 1, 1),
  (2, 'ROOT_ROT', 'Conifer root rot', 2, 1);



-- pat_disease_associations
INSERT INTO pat_disease_associations (id, species_id, host_id, disease_id, infection_mode, first_reported_year, primary_evidence_publication_id) VALUES
  (1, 5, 1, 1, 'biotrophic', 1843, NULL);



-- ord_agaricales_edibility
INSERT INTO ord_agaricales_edibility (id, species_id, edibility_class, preparation_notes, regional_tradition_country_id) VALUES
  (1, 1, 'deadly', 'Contains amatoxins. Onset 6-24h, hepatotoxic; no domestic processing renders safe.', 1),
  (2, 4, 'deadly', 'Contains amatoxins similar to Amanita phalloides; commonly mistaken for edible Galerina.', NULL),
  (3, 6, 'poisonous', 'Contains ibotenic acid / muscimol; psychoactive but toxic; traditionally detoxified in some regions.', 3);



-- ord_boletales_edibility
INSERT INTO ord_boletales_edibility (id, species_id, edibility_class, preparation_notes, regional_tradition_country_id) VALUES
  (1, 2, 'choice', 'Highly prized worldwide; commonly sold dried.', 1);



-- ord_agaricales_dna_barcoding_status
INSERT INTO ord_agaricales_dna_barcoding_status (id, species_id, its_sequenced, lsu_sequenced, rpb2_sequenced, ef1a_sequenced, genome_assembled, priority_for_sequencing_score) VALUES
  (1, 1, 1, 1, 1, 0, 1, 1),
  (2, 4, 1, 1, 0, 0, 1, 2),
  (3, 6, 1, 1, 1, 1, 1, 1);



COMMIT;