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@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+database/mycobase/mycobase.sqlite filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,43 @@
+---
+license: mit
+task_categories:
+- text-to-sql
+tags:
+- mycology
+- fungal-research
+- complex-schema
+- spider-format
+- bird-format
+pretty_name: MycoBase Text-to-SQL Dataset
+size_categories:
+- 100K<n<1M
+---
+
+# MycoBase: A Biologically Literate Text-to-SQL Dataset
+
+**MycoBase** is a synthetic but biologically accurate dataset designed for stress-testing Text-to-SQL systems. It represents a research information system for the study of fungi, covering everything from taxonomy and genomics to morphology and cultivation.
+
+## Dataset Highlights
+- **Schema Complexity**: 2,016 tables with over 9,000 foreign key relationships.
+- **Data Volume**: 320,270 rows of realistic mycology data.
+- **Realistic Names**: Includes tens of thousands of actual fungal species names, famous mycologists (authors), and scientific publication titles.
+- **Format**: Compatible with **Spider** and **BIRD** benchmark tools.
+
+## Repository Structure
+- `database/mycobase/mycobase.sqlite`: The SQLite database containing the full schema and data.
+- `tables.json`: Structural metadata (schema) in BIRD/Spider format.
+- `train.json`: Natural Language to SQL query pairs for training/evaluation.
+- `mycobase_benchmark_summary.csv`: A pipe-separated summary of questions, ground-truth SQL, and retrieval stats.
+- `csv_exports/`: Sample data for core tables (tax_species, specimens, etc.).
+- `mycobase_sqlite_schema.sql`: Full SQLite DDL script.
+
+## Example Questions
+- *"Which species in our database contain amatoxins, and at what concentrations?"*
+- *"Show me ITS sequences with their species and the herbarium voucher they came from."*
+- *"Which Agaricales species are classified as deadly, and what is the mean amatoxin concentration reported for each?"*
+
+## Dataset Generation
+This dataset was generated using the MycoBase core framework, ensuring biological literacy across 57 fungal orders. Every table and column is modeled after real-world research workflows in mycology.
+
+## License
+MIT

csv_exports/bio_compound_classes.csv

@@ -0,0 +1,5 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,ALK,Alkaloid,,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,PEPT,Peptide,,2,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,POLY,Polyketide,,3,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,TERP,Terpenoid,,4,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/bio_compounds.csv

@@ -0,0 +1,51 @@
+id,compound_class_id,preferred_name,iupac_name,inchi,inchi_key,smiles,cas_number,molecular_formula,monoisotopic_mass_da,logp,is_secondary_metabolite,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,2,alpha-Amanitin,,,,,23109-05-9,C39H54N10O14S,918.3592,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,2,beta-Amanitin,,,,,21150-22-1,C39H53N9O15S,919.3432,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,2,Phalloidin,,,,,17466-45-4,C35H48N8O11S,788.3163,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,1,Muscarine,,,,,300-54-9,C9H20NO2,174.1494,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+5,1,Ibotenic acid,,,,,2552-55-8,C5H6N2O4,158.0327,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+6,1,Psilocybin,,,,,520-52-5,C12H17N2O4P,284.0926,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+7,4,Ergosterol,,,,,57-87-4,C28H44O,396.3392,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+8,30,Synthetic preferred_name 0,Synthetic iupac_name 0,Synthetic inchi 0,Synthetic inchi_key 0,Synthetic smiles 0,Synthetic cas_number 0,Synthetic molecular_formula 0,82.25450223626181,14.23344761116972,0,2006-09-25,2018-05-19,1,1,1,690
+9,302,Synthetic preferred_name 1,Synthetic iupac_name 1,Synthetic inchi 1,Synthetic inchi_key 1,Synthetic smiles 1,Synthetic cas_number 1,Synthetic molecular_formula 1,73.70224151609843,10.129869004573308,1,2022-07-14,2024-09-10,1,1,1,74
+10,262,Synthetic preferred_name 2,Synthetic iupac_name 2,Synthetic inchi 2,Synthetic inchi_key 2,Synthetic smiles 2,Synthetic cas_number 2,Synthetic molecular_formula 2,4.267865656749953,73.64698704107204,0,2005-04-21,2007-04-21,1,1,1,91
+11,44,Synthetic preferred_name 3,Synthetic iupac_name 3,Synthetic inchi 3,Synthetic inchi_key 3,Synthetic smiles 3,Synthetic cas_number 3,Synthetic molecular_formula 3,26.980573427768242,35.15437028960508,1,2020-11-02,2024-03-16,1,1,0,738
+12,612,Synthetic preferred_name 4,Synthetic iupac_name 4,Synthetic inchi 4,Synthetic inchi_key 4,Synthetic smiles 4,Synthetic cas_number 4,Synthetic molecular_formula 4,47.8230983828109,70.4216865602062,1,2016-09-21,2021-11-06,1,1,0,331
+13,725,Synthetic preferred_name 5,Synthetic iupac_name 5,Synthetic inchi 5,Synthetic inchi_key 5,Synthetic smiles 5,Synthetic cas_number 5,Synthetic molecular_formula 5,89.32190739532018,75.17368507592367,1,2009-03-08,2017-12-18,1,1,0,902
+14,445,Synthetic preferred_name 6,Synthetic iupac_name 6,Synthetic inchi 6,Synthetic inchi_key 6,Synthetic smiles 6,Synthetic cas_number 6,Synthetic molecular_formula 6,79.34564937069405,57.548773766442906,1,2009-05-02,2011-07-02,1,1,1,222
+15,618,Synthetic preferred_name 7,Synthetic iupac_name 7,Synthetic inchi 7,Synthetic inchi_key 7,Synthetic smiles 7,Synthetic cas_number 7,Synthetic molecular_formula 7,45.03170326101956,61.09486864219406,0,2009-03-26,2023-08-09,1,1,0,970
+16,856,Synthetic preferred_name 8,Synthetic iupac_name 8,Synthetic inchi 8,Synthetic inchi_key 8,Synthetic smiles 8,Synthetic cas_number 8,Synthetic molecular_formula 8,49.65648416819709,27.946395987233842,1,2020-03-22,2020-02-18,1,1,0,579
+17,614,Synthetic preferred_name 9,Synthetic iupac_name 9,Synthetic inchi 9,Synthetic inchi_key 9,Synthetic smiles 9,Synthetic cas_number 9,Synthetic molecular_formula 9,93.41573681825024,56.37882860750752,0,2004-05-14,2000-04-15,1,1,1,152
+18,54,Synthetic preferred_name 10,Synthetic iupac_name 10,Synthetic inchi 10,Synthetic inchi_key 10,Synthetic smiles 10,Synthetic cas_number 10,Synthetic molecular_formula 10,62.332074078251864,50.61133878897748,1,2007-09-11,2022-05-22,1,1,1,446
+19,979,Synthetic preferred_name 11,Synthetic iupac_name 11,Synthetic inchi 11,Synthetic inchi_key 11,Synthetic smiles 11,Synthetic cas_number 11,Synthetic molecular_formula 11,1.7207191583038,82.2264257827089,0,2002-09-12,2006-03-27,1,1,0,597
+20,429,Synthetic preferred_name 12,Synthetic iupac_name 12,Synthetic inchi 12,Synthetic inchi_key 12,Synthetic smiles 12,Synthetic cas_number 12,Synthetic molecular_formula 12,1.5390366272474045,66.28179943264816,0,2009-07-25,2020-03-27,1,1,1,858
+21,993,Synthetic preferred_name 13,Synthetic iupac_name 13,Synthetic inchi 13,Synthetic inchi_key 13,Synthetic smiles 13,Synthetic cas_number 13,Synthetic molecular_formula 13,54.395887932063005,47.84129196801891,1,2015-05-18,2017-02-15,1,1,0,418
+22,674,Synthetic preferred_name 14,Synthetic iupac_name 14,Synthetic inchi 14,Synthetic inchi_key 14,Synthetic smiles 14,Synthetic cas_number 14,Synthetic molecular_formula 14,91.80214512307461,58.63847798368357,1,2004-05-18,2006-12-21,1,1,0,68
+23,543,Synthetic preferred_name 15,Synthetic iupac_name 15,Synthetic inchi 15,Synthetic inchi_key 15,Synthetic smiles 15,Synthetic cas_number 15,Synthetic molecular_formula 15,52.90054235669174,75.79789420331869,0,2018-12-13,2020-11-21,1,1,1,612
+24,758,Synthetic preferred_name 16,Synthetic iupac_name 16,Synthetic inchi 16,Synthetic inchi_key 16,Synthetic smiles 16,Synthetic cas_number 16,Synthetic molecular_formula 16,54.54299632385775,48.945632827130645,1,2024-08-09,2007-11-26,1,1,0,801
+25,12,Synthetic preferred_name 17,Synthetic iupac_name 17,Synthetic inchi 17,Synthetic inchi_key 17,Synthetic smiles 17,Synthetic cas_number 17,Synthetic molecular_formula 17,2.351119177081031,26.20331096863384,0,2001-07-26,2019-03-15,1,1,0,256
+26,350,Synthetic preferred_name 18,Synthetic iupac_name 18,Synthetic inchi 18,Synthetic inchi_key 18,Synthetic smiles 18,Synthetic cas_number 18,Synthetic molecular_formula 18,20.444570844779932,27.379280569756187,0,2015-03-16,2021-10-12,1,1,1,590
+27,750,Synthetic preferred_name 19,Synthetic iupac_name 19,Synthetic inchi 19,Synthetic inchi_key 19,Synthetic smiles 19,Synthetic cas_number 19,Synthetic molecular_formula 19,82.33490524214905,23.422855292265265,1,2003-09-10,2016-10-15,1,1,0,14
+28,312,Synthetic preferred_name 20,Synthetic iupac_name 20,Synthetic inchi 20,Synthetic inchi_key 20,Synthetic smiles 20,Synthetic cas_number 20,Synthetic molecular_formula 20,24.90313248201462,74.4361795785526,0,2002-11-09,2011-12-17,1,1,0,199
+29,211,Synthetic preferred_name 21,Synthetic iupac_name 21,Synthetic inchi 21,Synthetic inchi_key 21,Synthetic smiles 21,Synthetic cas_number 21,Synthetic molecular_formula 21,57.022482856494115,45.16461660829758,1,2006-05-25,2009-04-17,1,1,0,162
+30,62,Synthetic preferred_name 22,Synthetic iupac_name 22,Synthetic inchi 22,Synthetic inchi_key 22,Synthetic smiles 22,Synthetic cas_number 22,Synthetic molecular_formula 22,23.458928612049434,25.46630663407232,1,2001-09-27,2021-10-12,1,1,0,190
+31,567,Synthetic preferred_name 23,Synthetic iupac_name 23,Synthetic inchi 23,Synthetic inchi_key 23,Synthetic smiles 23,Synthetic cas_number 23,Synthetic molecular_formula 23,98.60346507899561,68.11969110112838,0,2014-01-11,2019-04-12,1,1,1,412
+32,237,Synthetic preferred_name 24,Synthetic iupac_name 24,Synthetic inchi 24,Synthetic inchi_key 24,Synthetic smiles 24,Synthetic cas_number 24,Synthetic molecular_formula 24,18.07846976545543,54.61751920728631,0,2023-08-28,2015-05-17,1,1,0,231
+33,455,Synthetic preferred_name 25,Synthetic iupac_name 25,Synthetic inchi 25,Synthetic inchi_key 25,Synthetic smiles 25,Synthetic cas_number 25,Synthetic molecular_formula 25,97.45327125053186,30.09793247089557,1,2012-12-18,2006-07-10,1,1,1,515
+34,588,Synthetic preferred_name 26,Synthetic iupac_name 26,Synthetic inchi 26,Synthetic inchi_key 26,Synthetic smiles 26,Synthetic cas_number 26,Synthetic molecular_formula 26,94.0798888930071,10.776442823635868,1,2016-07-22,2007-02-21,1,1,0,645
+35,735,Synthetic preferred_name 27,Synthetic iupac_name 27,Synthetic inchi 27,Synthetic inchi_key 27,Synthetic smiles 27,Synthetic cas_number 27,Synthetic molecular_formula 27,71.68422357550213,68.76212633986455,1,2013-09-14,2022-08-28,1,1,0,145
+36,358,Synthetic preferred_name 28,Synthetic iupac_name 28,Synthetic inchi 28,Synthetic inchi_key 28,Synthetic smiles 28,Synthetic cas_number 28,Synthetic molecular_formula 28,83.84501756630361,19.295539566729527,1,2018-08-17,2010-05-21,1,1,0,459
+37,366,Synthetic preferred_name 29,Synthetic iupac_name 29,Synthetic inchi 29,Synthetic inchi_key 29,Synthetic smiles 29,Synthetic cas_number 29,Synthetic molecular_formula 29,13.34920034959615,2.9547304467311464,0,2020-11-15,2010-03-04,1,1,1,922
+38,312,Synthetic preferred_name 30,Synthetic iupac_name 30,Synthetic inchi 30,Synthetic inchi_key 30,Synthetic smiles 30,Synthetic cas_number 30,Synthetic molecular_formula 30,38.79073621392567,62.244062270269495,0,2018-05-24,2014-03-27,1,1,0,674
+39,522,Synthetic preferred_name 31,Synthetic iupac_name 31,Synthetic inchi 31,Synthetic inchi_key 31,Synthetic smiles 31,Synthetic cas_number 31,Synthetic molecular_formula 31,33.38458273519668,89.6274428137773,0,2010-08-02,2023-07-10,1,1,0,343
+40,740,Synthetic preferred_name 32,Synthetic iupac_name 32,Synthetic inchi 32,Synthetic inchi_key 32,Synthetic smiles 32,Synthetic cas_number 32,Synthetic molecular_formula 32,74.47702885105873,70.62085539820758,1,2019-09-21,2006-02-22,1,1,1,522
+41,459,Synthetic preferred_name 33,Synthetic iupac_name 33,Synthetic inchi 33,Synthetic inchi_key 33,Synthetic smiles 33,Synthetic cas_number 33,Synthetic molecular_formula 33,35.593378336709485,69.35977798748799,0,2009-04-11,2008-10-14,1,1,0,575
+42,314,Synthetic preferred_name 34,Synthetic iupac_name 34,Synthetic inchi 34,Synthetic inchi_key 34,Synthetic smiles 34,Synthetic cas_number 34,Synthetic molecular_formula 34,63.301928577194175,5.248028371714349,1,2013-04-02,2005-10-23,1,1,1,970
+43,433,Synthetic preferred_name 35,Synthetic iupac_name 35,Synthetic inchi 35,Synthetic inchi_key 35,Synthetic smiles 35,Synthetic cas_number 35,Synthetic molecular_formula 35,59.94379883210063,73.3103438707346,1,2009-04-16,2009-11-08,1,1,0,324
+44,16,Synthetic preferred_name 36,Synthetic iupac_name 36,Synthetic inchi 36,Synthetic inchi_key 36,Synthetic smiles 36,Synthetic cas_number 36,Synthetic molecular_formula 36,69.17052791465429,46.036158323381215,1,2008-10-11,2020-12-01,1,1,0,926
+45,541,Synthetic preferred_name 37,Synthetic iupac_name 37,Synthetic inchi 37,Synthetic inchi_key 37,Synthetic smiles 37,Synthetic cas_number 37,Synthetic molecular_formula 37,83.55029513871705,87.59883688718496,0,2008-02-04,2001-02-22,1,1,1,118
+46,78,Synthetic preferred_name 38,Synthetic iupac_name 38,Synthetic inchi 38,Synthetic inchi_key 38,Synthetic smiles 38,Synthetic cas_number 38,Synthetic molecular_formula 38,52.03747734045238,51.20231500501947,0,2018-10-19,2010-12-17,1,1,1,268
+47,771,Synthetic preferred_name 39,Synthetic iupac_name 39,Synthetic inchi 39,Synthetic inchi_key 39,Synthetic smiles 39,Synthetic cas_number 39,Synthetic molecular_formula 39,22.65030897083181,0.7134243386645842,1,2021-06-15,2014-12-13,1,1,0,323
+48,276,Synthetic preferred_name 40,Synthetic iupac_name 40,Synthetic inchi 40,Synthetic inchi_key 40,Synthetic smiles 40,Synthetic cas_number 40,Synthetic molecular_formula 40,45.94952479262929,75.36847746713327,0,2020-10-05,2008-01-04,1,1,1,91
+49,378,Synthetic preferred_name 41,Synthetic iupac_name 41,Synthetic inchi 41,Synthetic inchi_key 41,Synthetic smiles 41,Synthetic cas_number 41,Synthetic molecular_formula 41,0.2291589994881213,24.68560836936076,0,2012-12-17,2004-10-21,1,1,0,524
+50,546,Synthetic preferred_name 42,Synthetic iupac_name 42,Synthetic inchi 42,Synthetic inchi_key 42,Synthetic smiles 42,Synthetic cas_number 42,Synthetic molecular_formula 42,21.872648758070174,6.048661716645423,0,2005-04-07,2016-12-09,1,1,1,301

csv_exports/bio_species_compound_occurrences.csv

@@ -0,0 +1,7 @@
+id,species_id,compound_id,specimen_id,concentration_mg_per_g,detection_method,publication_id,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,1,1,1,0.45,HPLC-MS,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,1,2,1,0.29,HPLC-MS,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,1,3,1,0.082,HPLC-MS,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,4,1,5,0.041,HPLC-MS,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+5,6,5,,0.6,HPLC-UV,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+6,6,6,,0.008,HPLC-UV,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/bio_toxin_amatoxins.csv

@@ -0,0 +1,3 @@
+id,compound_id,ld50_mg_per_kg_mouse,primary_target_organ,symptom_onset_hours_min,symptom_onset_hours_max,antidote_summary,publication_id,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,1,0.1,liver,6.0,24.0,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,2,0.2,liver,6.0,24.0,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/eco_iucn_assessments.csv

@@ -0,0 +1,4 @@
+id,species_id,assessment_year,category,criteria,rationale,publication_id,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,1,2019,LC,,Widespread in Europe and North America.,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,2,2019,LC,,Common across the Holarctic.,2,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,5,2020,VU,,Over-collection for traditional medicine; declining populations.,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/eco_phenology_observations.csv

@@ -0,0 +1,5 @@
+id,species_id,locality_id,observation_year,first_fruit_doy,peak_fruit_doy,last_fruit_doy,season_id,data_source,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,1,1,2022,220,256,295,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,2,2,2021,240,275,310,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,3,1,2022,235,268,302,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,5,3,2023,121,145,180,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/gen_sequencing_platforms.csv

@@ -0,0 +1,4 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,ILL_NOV,Illumina NovaSeq 6000,,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,PB_SEQ,PacBio Sequel IIe,,2,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,ONT_PROM,Oxford Nanopore PromethION,,3,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/geo_biomes.csv

@@ -0,0 +1,6 @@
+id,code,label,description,display_order,is_active,typical_temperature_c,typical_precipitation_mm,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,TBMF,Temperate broadleaf & mixed forest,,1,1,10.0,900.0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,TCF,Temperate coniferous forest,,2,1,6.0,1200.0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,TRF,Tropical & subtropical moist broadleaf forest,,3,1,24.0,2200.0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,BORF,Boreal forest / taiga,,4,1,-1.0,500.0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+5,MOMG,Montane grassland & shrubland,,5,1,8.0,700.0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/geo_continents.csv

@@ -0,0 +1,8 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,EU,Europe,,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,NA,North America,,2,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,SA,South America,,3,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,AS,Asia,,4,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+5,AF,Africa,,5,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+6,OC,Oceania,,6,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+7,AN,Antarctica,,7,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/geo_countries.csv

@@ -0,0 +1,11 @@
+id,iso_alpha2,iso_alpha3,iso_numeric,name,official_name,continent_id,capital,area_km2,centroid_lat,centroid_lon,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,PL,POL,616,Poland,,1,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,US,USA,840,United States,,2,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,JP,JPN,392,Japan,,4,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,BR,BRA,76,Brazil,,3,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+5,SE,SWE,752,Sweden,,1,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+6,IN,IND,356,India,,4,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+7,DE,DEU,276,Germany,,1,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+8,GB,GBR,826,United Kingdom,,1,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+9,AU,AUS,36,Australia,,6,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+10,CN,CHN,156,China,,4,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/geo_localities.csv

@@ -0,0 +1,6 @@
+id,uuid,name,country_id,subdivision_id,ecoregion_id,decimal_latitude,decimal_longitude,coordinate_uncertainty_m,elevation_m,depth_m,georeference_method,georeference_source,georeferenced_by_user_id,georeferenced_at,is_type_locality,notes,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,aaaa1111-1111-1111-1111-111111111111,"Białowieża Forest, oak-hornbeam stand BPN-A3",1,,,52.7,23.87,,165.0,,,,,,0,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,aaaa2222-2222-2222-2222-222222222222,"Mt. Hood National Forest, Oregon, Cascade conifer slope",2,,,45.37,-121.69,,1340.0,,,,,,0,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,aaaa3333-3333-3333-3333-333333333333,"Yakushima island, evergreen broadleaf forest near Shiratani",3,,,30.32,130.55,,620.0,,,,,,0,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,aaaa4444-4444-4444-4444-444444444444,"Atlantic Forest fragment, Serra do Mar, Cubatão",4,,,-23.86,-46.42,,380.0,,,,,,0,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+5,aaaa5555-5555-5555-5555-555555555555,"Abisko subarctic taiga, birch–pine ecotone",5,,,68.36,18.78,,410.0,,,,,,0,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/lit_journals.csv

@@ -0,0 +1,4 @@
+id,title,abbreviation,issn_print,issn_online,publisher,country_id,first_year,last_year,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,Mycologia,Mycologia,,1557-2536,Mycological Society of America,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,Persoonia,Persoonia,,1878-9080,Naturalis,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,Fungal Diversity,Fungal Divers.,,1878-9129,Springer Nature,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/lit_publication_types.csv

@@ -0,0 +1,5 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,JART,Journal article,,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,BOOK,Book,,2,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,MONO,Monograph,,3,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,THES,Thesis,,4,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/lit_publications.csv

@@ -0,0 +1,4 @@
+id,uuid,publication_type_id,title,year,journal_id,volume,issue,page_start,page_end,doi,isbn,url,abstract,language_code,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+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,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+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,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,cccc3333-3333-3333-3333-333333333333,3,Monograph of Russula in the Pacific Northwest,2017,,,,,,,,,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/mor_chemical_reagents.csv

@@ -0,0 +1,5 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,KOH3,3% potassium hydroxide,,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,MELZ,Melzer's reagent,,2,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,NH4OH,Ammonium hydroxide,,3,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,FESO4,Iron(II) sulfate,,4,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/mor_spore_measurements.csv

@@ -0,0 +1,5 @@
+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,measured_at,measured_by_person_id,publication_id,excludes_apiculus,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,1,1,8.5,11.0,9.4,7.0,9.0,8.1,1.05,1.3,1.16,30,2,,,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,2,2,13.0,17.5,15.2,4.5,6.0,5.3,2.55,3.2,2.87,50,1,,,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,3,3,8.0,11.0,9.5,7.0,9.5,8.2,1.05,1.25,1.16,25,2,,,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,4,5,10.0,14.0,12.0,3.0,4.0,3.5,3.0,4.0,3.4,30,1,,,,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/ord_agaricales_dna_barcoding_status.csv

@@ -0,0 +1,4 @@
+id,species_id,its_sequenced,lsu_sequenced,rpb2_sequenced,ef1a_sequenced,genome_assembled,priority_for_sequencing_score,notes,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,1,1,1,1,0,1,1,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,4,1,1,0,0,1,2,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,6,1,1,1,1,1,1,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/ord_agaricales_edibility.csv

@@ -0,0 +1,4 @@
+id,species_id,edibility_class,preparation_notes,regional_tradition_country_id,notes,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,1,deadly,"Contains amatoxins. Onset 6-24h, hepatotoxic; no domestic processing renders safe.",1,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,4,deadly,Contains amatoxins similar to Amanita phalloides; commonly mistaken for edible Galerina.,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,6,poisonous,Contains ibotenic acid / muscimol; psychoactive but toxic; traditionally detoxified in some regions.,3,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/ord_boletales_edibility.csv

@@ -0,0 +1,2 @@
+id,species_id,edibility_class,preparation_notes,regional_tradition_country_id,notes,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,2,choice,Highly prized worldwide; commonly sold dried.,1,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/pat_disease_associations.csv

@@ -0,0 +1,2 @@
+id,species_id,host_id,disease_id,infection_mode,first_reported_year,primary_evidence_publication_id,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,5,1,1,biotrophic,1843,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/pat_diseases.csv

@@ -0,0 +1,3 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,ENTPAR,Entomopathogenic infection (fungal),,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,ROOT_ROT,Conifer root rot,,2,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/pat_host_organism_kingdoms.csv

@@ -0,0 +1,5 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,PLANT,Plant,,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,AVERT,Animal (vertebrate),,2,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,AINV,Animal (invertebrate),,3,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,FUNG,Fungus,,4,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/pat_host_organisms.csv

@@ -0,0 +1,3 @@
+id,host_kingdom_id,host_family,host_genus,host_species,common_name,economic_importance_note,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,3,Hepialidae,Thitarodes,armoricanus,ghost moth larva,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,1,Pinaceae,Pinus,sylvestris,Scots pine,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/people_herbaria.csv

@@ -0,0 +1,4 @@
+id,institution_id,ih_code,name,specimen_count_estimate,focus_taxa,contact_user_id,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,1,K,Kew Mycology Herbarium,1250000,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,2,NY,NYBG William and Lynda Steere Herbarium,8000000,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,3,L,Naturalis Cryptogamic Herbarium,2000000,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/people_institutions.csv

@@ -0,0 +1,6 @@
+id,name,acronym,ror_id,country_id,website_url,address,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,"Royal Botanic Gardens, Kew",RBG-K,,8,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,New York Botanical Garden,NYBG,,2,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,Naturalis Biodiversity Center,NL,,7,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,Indian Institute of Science,IISc,,6,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+5,"Polish Academy of Sciences, Białowieża Geobotanical Station",PAS-BIA,,1,,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/spc_collection_events.csv

@@ -0,0 +1,4 @@
+id,uuid,event_date,event_time_start,event_time_end,locality_id,collection_method_id,expedition_id,habitat_summary,weather_summary,temperature_c,humidity_pct,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,eeee0001-0001-0001-0001-000000000001,2022-09-12,,,1,,,"Mature oak-hornbeam stand, mossy logs",,14.2,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,eeee0002-0002-0002-0002-000000000002,2021-10-04,,,2,,,"Douglas-fir canopy, deep litter on north slope",,9.5,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,eeee0003-0003-0003-0003-000000000003,2023-08-15,,,3,,,Sphagnum moss carpet under Cryptomeria,,19.0,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/spc_preservation_methods.csv

@@ -0,0 +1,5 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,DRIED,Dried,,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,ETOH,70% ethanol,,2,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,FROZEN,Frozen at -80 C,,3,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,SILICA,Silica gel,,4,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/spc_specimens.csv

@@ -0,0 +1,6 @@
+id,uuid,catalog_number,herbarium_id,collection_event_id,collector_number,primary_collector_person_id,preservation_method_id,growth_substrate_id,substrate_detail,identified_species_id,identified_at_rank,identification_confidence,identified_by_person_id,identified_at,is_type_specimen,storage_location,condition_score,notes,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,ffff0001-0001-0001-0001-000000000001,K(M)281044,1,1,EGC-2022-103,3,1,,,1,species,expert,,,0,,5,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,ffff0002-0002-0002-0002-000000000002,NY01234567,2,2,JK-217,3,1,,,2,species,expert,,,0,,4,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,ffff0003-0003-0003-0003-000000000003,NY01234589,2,2,JK-218,3,1,,,3,species,verified,,,0,,4,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,ffff0004-0004-0004-0004-000000000004,L0455123,3,3,RK-2023-08-15-04,3,1,,,5,species,expert,,,1,,5,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+5,ffff0005-0005-0005-0005-000000000005,K(M)281099,1,1,EGC-2022-104,3,1,,,4,species,tentative,,,0,,3,,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/sys_users.csv

@@ -0,0 +1,5 @@
+id,uuid,username,email,display_name,password_hash,orcid,primary_institution_id,is_active,is_curator,last_login_at,created_at,updated_at
+1,11111111-1111-1111-1111-111111111111,egc,egc@bot.example.org,Elsie G. Curtis,,,,1,1,,2026-05-06 09:03:33,2026-05-06 09:03:33
+2,22222222-2222-2222-2222-222222222222,rkato,rkato@myco.example.jp,Ryo Kato,,,,1,1,,2026-05-06 09:03:33,2026-05-06 09:03:33
+3,33333333-3333-3333-3333-333333333333,mlind,m.lindberg@gen.example.se,Märta Lindberg,,,,1,0,,2026-05-06 09:03:33,2026-05-06 09:03:33
+4,44444444-4444-4444-4444-444444444444,asankar,a.sankaranarayanan@iisc.example.in,Anjali Sankaranarayanan,,,,1,1,,2026-05-06 09:03:33,2026-05-06 09:03:33

csv_exports/tax_classes.csv

@@ -0,0 +1,3 @@
+id,uuid,scientific_name,authority,year_published,protologue_publication_id,nomenclatural_code_id,status_id,accepted_id,parent_subphylum_id,ipni_id,mycobank_number,index_fungorum_id,etymology,description_morphology,type_locality_id,is_type_genus,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,dddd0003-0001-0001-0001-000000000001,Agaricomycetes,Doweld,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,dddd0003-0001-0001-0001-000000000002,Sordariomycetes,O.E. Erikss. & Winka,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/tax_families.csv

@@ -0,0 +1,5 @@
+id,uuid,scientific_name,authority,year_published,protologue_publication_id,nomenclatural_code_id,status_id,accepted_id,parent_suborder_id,ipni_id,mycobank_number,index_fungorum_id,etymology,description_morphology,type_locality_id,is_type_genus,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,dddd0005-0001-0001-0001-000000000001,Amanitaceae,E.-J. Gilbert,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,dddd0005-0001-0001-0001-000000000002,Boletaceae,Chevall.,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,dddd0005-0001-0001-0001-000000000003,Russulaceae,Lotsy,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,dddd0005-0001-0001-0001-000000000004,Strophariaceae,Singer & A.H. Sm.,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/tax_genera.csv

@@ -0,0 +1,6 @@
+id,uuid,scientific_name,authority,year_published,protologue_publication_id,nomenclatural_code_id,status_id,accepted_id,parent_tribe_id,ipni_id,mycobank_number,index_fungorum_id,etymology,description_morphology,type_locality_id,is_type_genus,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,dddd0006-0001-0001-0001-000000000001,Amanita,Pers.,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,dddd0006-0001-0001-0001-000000000002,Boletus,L.,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,dddd0006-0001-0001-0001-000000000003,Russula,Pers.,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,dddd0006-0001-0001-0001-000000000004,Galerina,Earle,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+5,dddd0006-0001-0001-0001-000000000005,Ophiocordyceps,Petch,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/tax_kingdoms.csv

@@ -0,0 +1,2 @@
+id,uuid,scientific_name,authority,year_published,protologue_publication_id,nomenclatural_code_id,status_id,accepted_id,ipni_id,mycobank_number,index_fungorum_id,etymology,description_morphology,type_locality_id,is_type_genus,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,dddd0001-0001-0001-0001-000000000001,Fungi,Bartling,1830,,1,1,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/tax_nomenclatural_codes.csv

@@ -0,0 +1,2 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,ICNAFP,"International Code of Nomenclature for algae, fungi, and plants",,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/tax_orders.csv

@@ -0,0 +1,5 @@
+id,uuid,scientific_name,authority,year_published,protologue_publication_id,nomenclatural_code_id,status_id,accepted_id,parent_subclass_id,ipni_id,mycobank_number,index_fungorum_id,etymology,description_morphology,type_locality_id,is_type_genus,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,dddd0004-0001-0001-0001-000000000001,Agaricales,Underw.,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,dddd0004-0001-0001-0001-000000000002,Boletales,E.-J. Gilbert,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,dddd0004-0001-0001-0001-000000000003,Russulales,"Kreisel ex P.M. Kirk, P.F. Cannon & J.C. David",,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,dddd0004-0001-0001-0001-000000000004,Hypocreales,Lindau,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/tax_phyla.csv

@@ -0,0 +1,3 @@
+id,uuid,scientific_name,authority,year_published,protologue_publication_id,nomenclatural_code_id,status_id,accepted_id,parent_subkingdom_id,ipni_id,mycobank_number,index_fungorum_id,etymology,description_morphology,type_locality_id,is_type_genus,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,dddd0002-0001-0001-0001-000000000001,Basidiomycota,R.T. Moore,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,dddd0002-0001-0001-0001-000000000002,Ascomycota,Caval.-Sm.,,,1,1,,,,,,,,,0,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

csv_exports/tax_taxonomic_status.csv

@@ -0,0 +1,5 @@
+id,code,label,description,display_order,is_active,created_at,updated_at,created_by_user_id,updated_by_user_id,is_deleted,row_version
+1,ACCEPTED,Accepted,,1,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+2,SYNONYM,Synonym,,2,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+3,DOUBTFUL,Doubtful (nomen dubium),,3,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1
+4,MISAPPLIED,Misapplied name,,4,1,2026-05-06 09:03:33,2026-05-06 09:03:33,,,0,1

database/mycobase/mycobase.sqlite

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:281859c7e9385b70333e1f23b991f54550163a411733ca7924042be6cbd591fa
+size 99028992

mycobase_benchmark_summary.csv

@@ -0,0 +1,26 @@
+qustion in natural lang|sql query ground truth|colmns retived|rows retirved
+"Which species in our database contain amatoxins, and at what
+> concentrations?"|"SELECT s.scientific_name, c.preferred_name, o.concentration_mg_per_g
+FROM bio_species_compound_occurrences o
+JOIN tax_species s ON s.id = o.species_id
+JOIN bio_compounds c ON c.id = o.compound_id
+JOIN bio_toxin_amatoxins t ON t.compound_id = c.id
+ORDER BY s.scientific_name, c.preferred_name;"|scientific_name, preferred_name, concentration_mg_per_g|3
+"Show me ITS sequences with their species and the herbarium voucher
+> they came from."|"SELECT s.scientific_name,
+       h.ih_code || ' ' || sp.catalog_number AS voucher,
+       seq.length_bp, seq.gc_content_pct
+FROM gen_sequences seq
+JOIN spc_specimens sp ON sp.id = seq.specimen_id
+JOIN people_herbaria h ON h.id = sp.herbarium_id
+JOIN tax_species s ON s.id = sp.identified_species_id
+WHERE seq.locus = 'its';"|scientific_name, voucher, length_bp, gc_content_pct|4
+"Which Agaricales species are classified as deadly, and what is the
+> mean amatoxin concentration reported for each?"|"SELECT s.scientific_name, e.edibility_class,
+       AVG(o.concentration_mg_per_g) AS mean_amatoxin
+FROM ord_agaricales_edibility e
+JOIN tax_species s ON s.id = e.species_id
+LEFT JOIN bio_species_compound_occurrences o ON o.species_id = s.id
+LEFT JOIN bio_toxin_amatoxins t ON t.compound_id = o.compound_id
+WHERE e.edibility_class = 'deadly'
+GROUP BY s.scientific_name, e.edibility_class;"|scientific_name, edibility_class, mean_amatoxin|2

mycobase_dataset_summary.csv

@@ -0,0 +1,2017 @@
+Table Name,Row Count
+sys_users,50
+sys_roles,49
+sys_user_roles,0
+sys_permissions,48
+sys_role_permissions,0
+sys_api_keys,50
+sys_settings,50
+sys_audit_log,50
+sys_jobs,14
+geo_continents,49
+geo_countries,49
+geo_subdivisions,50
+geo_biomes,49
+geo_ecoregions,49
+geo_climate_zones,49
+geo_soil_orders,47
+geo_vegetation_types,48
+geo_localities,50
+geo_locality_aliases,50
+people_persons,1005
+people_institutions,50
+people_herbaria,49
+people_affiliations,50
+people_role_types,49
+lit_publication_types,48
+lit_journals,50
+lit_publications,1003
+lit_authorships,50
+lit_keywords,50
+lit_publication_keywords,0
+tax_nomenclatural_codes,50
+tax_taxonomic_status,48
+tax_type_designation_kinds,50
+tax_kingdoms,50
+tax_subkingdoms,50
+tax_phyla,50
+tax_subphyla,50
+tax_classes,50
+tax_subclasses,50
+tax_orders,50
+tax_suborders,50
+tax_families,50
+tax_subfamilies,50
+tax_tribes,50
+tax_genera,50
+tax_subgenera,50
+tax_sections,50
+tax_species,1006
+tax_subspecies,50
+tax_varieties,50
+tax_forms,50
+tax_synonymies,0
+tax_common_names,50
+tax_type_designations,50
+tax_revisions,50
+spc_preservation_methods,50
+spc_collection_methods,50
+spc_growth_substrates,50
+spc_collection_events,50
+spc_collection_event_collectors,0
+spc_specimens,5
+spc_identification_history,50
+spc_specimen_duplicates,50
+spc_loans,0
+spc_loan_specimens,0
+spc_specimen_publications,0
+spc_specimen_images,50
+mor_color_standards,49
+mor_color_chips,50
+mor_chemical_reagents,49
+mor_spore_measurements,50
+mor_states_pileus_shape,48
+mor_obs_pileus_shape,50
+mor_states_pileus_surface,47
+mor_obs_pileus_surface,50
+mor_states_pileus_margin,48
+mor_obs_pileus_margin,50
+mor_states_pileus_color,50
+mor_obs_pileus_color,50
+mor_states_hymenophore_type,50
+mor_obs_hymenophore_type,50
+mor_states_lamella_attachment,49
+mor_obs_lamella_attachment,50
+mor_states_lamella_spacing,49
+mor_obs_lamella_spacing,50
+mor_states_lamella_color,50
+mor_obs_lamella_color,50
+mor_states_pore_shape,50
+mor_obs_pore_shape,50
+mor_obs_pore_density_per_mm,50
+mor_obs_tubes_length,50
+mor_states_teeth_shape,49
+mor_obs_teeth_shape,50
+mor_states_stipe_shape,47
+mor_obs_stipe_shape,50
+mor_states_stipe_surface,48
+mor_obs_stipe_surface,50
+mor_states_stipe_color,50
+mor_obs_stipe_color,50
+mor_states_stipe_base_form,48
+mor_obs_stipe_base_form,50
+mor_states_annulus_form,50
+mor_obs_annulus_form,50
+mor_states_volva_form,49
+mor_obs_volva_form,50
+mor_states_flesh_color,49
+mor_obs_flesh_color,50
+mor_states_flesh_color_change,48
+mor_obs_flesh_color_change,50
+mor_states_smell_character,46
+mor_obs_smell_character,50
+mor_states_taste_character,49
+mor_obs_taste_character,50
+mor_states_latex_color,50
+mor_obs_latex_color,50
+mor_states_latex_color_change,50
+mor_obs_latex_color_change,50
+mor_states_spore_shape,50
+mor_obs_spore_shape,50
+mor_states_spore_ornamentation,49
+mor_obs_spore_ornamentation,50
+mor_states_spore_color_in_mass,48
+mor_obs_spore_color_in_mass,50
+mor_states_spore_color_in_koh,50
+mor_obs_spore_color_in_koh,50
+mor_states_spore_dextrinoid_reaction,49
+mor_obs_spore_dextrinoid_reaction,50
+mor_states_spore_germ_pore_present,50
+mor_obs_spore_germ_pore_present,50
+mor_states_basidium_shape,50
+mor_obs_basidium_shape,50
+mor_obs_basidium_n_spores,50
+mor_states_ascus_type,48
+mor_obs_ascus_type,50
+mor_states_ascus_apical_apparatus,50
+mor_obs_ascus_apical_apparatus,50
+mor_states_paraphysis_shape,49
+mor_obs_paraphysis_shape,50
+mor_states_cystidium_location,48
+mor_obs_cystidium_location,50
+mor_states_cystidium_shape,47
+mor_obs_cystidium_shape,50
+mor_states_hyphal_system,49
+mor_obs_hyphal_system,50
+mor_states_hyphal_clamp_connections,49
+mor_obs_hyphal_clamp_connections,50
+mor_states_hyphal_inflation,50
+mor_obs_hyphal_inflation,50
+mor_states_subhymenium_structure,47
+mor_obs_subhymenium_structure,50
+mor_states_trama_type,50
+mor_obs_trama_type,50
+mor_states_pileipellis_type,49
+mor_obs_pileipellis_type,50
+mor_states_rhizomorph_anatomy,46
+mor_obs_rhizomorph_anatomy,50
+mor_states_conidium_shape,48
+mor_obs_conidium_shape,50
+mor_states_conidiogenous_cell_type,49
+mor_obs_conidiogenous_cell_type,50
+mor_chemical_reactions,50
+eco_habitat_types,47
+eco_substrate_types,48
+eco_phenology_seasons,49
+eco_species_habitat_associations,50
+eco_species_substrate_associations,50
+eco_mycorrhiza_types,50
+eco_plant_partners,50
+eco_mycorrhiza_ectomycorrhizal,50
+eco_mycorrhiza_arbuscular,50
+eco_mycorrhiza_ericoid,50
+eco_mycorrhiza_orchid,50
+eco_mycorrhiza_monotropoid,50
+eco_mycorrhiza_arbutoid,50
+eco_mycorrhiza_ectendomycorrhizal,50
+eco_phenology_observations,9
+eco_iucn_assessments,3
+gen_sequencing_platforms,50
+gen_library_kit_types,48
+gen_assembly_software,50
+gen_alignment_software,46
+gen_dna_extracts,48
+gen_libraries,47
+gen_sequencing_runs,49
+gen_run_libraries,0
+gen_sequences,1004
+gen_assemblies,49
+gen_genes,0
+gen_proteins,50
+gen_orthogroups,48
+gen_orthogroup_members,0
+gen_variants,0
+gen_marker_its_sequences,50
+gen_marker_its_alignments,49
+gen_marker_its_alignment_members,0
+gen_marker_its_consensus,50
+gen_marker_lsu_sequences,50
+gen_marker_lsu_alignments,50
+gen_marker_lsu_alignment_members,0
+gen_marker_lsu_consensus,50
+gen_marker_ssu_sequences,50
+gen_marker_ssu_alignments,47
+gen_marker_ssu_alignment_members,0
+gen_marker_ssu_consensus,50
+gen_marker_rpb1_sequences,50
+gen_marker_rpb1_alignments,50
+gen_marker_rpb1_alignment_members,0
+gen_marker_rpb1_consensus,49
+gen_marker_rpb2_sequences,50
+gen_marker_rpb2_alignments,48
+gen_marker_rpb2_alignment_members,0
+gen_marker_rpb2_consensus,50
+gen_marker_ef1a_sequences,50
+gen_marker_ef1a_alignments,50
+gen_marker_ef1a_alignment_members,0
+gen_marker_ef1a_consensus,50
+gen_marker_tub2_sequences,50
+gen_marker_tub2_alignments,48
+gen_marker_tub2_alignment_members,0
+gen_marker_tub2_consensus,50
+gen_marker_mcm7_sequences,50
+gen_marker_mcm7_alignments,50
+gen_marker_mcm7_alignment_members,0
+gen_marker_mcm7_consensus,50
+gen_marker_act_sequences,50
+gen_marker_act_alignments,50
+gen_marker_act_alignment_members,0
+gen_marker_act_consensus,50
+gen_marker_cal_sequences,50
+gen_marker_cal_alignments,50
+gen_marker_cal_alignment_members,0
+gen_marker_cal_consensus,50
+gen_marker_gpd_sequences,50
+gen_marker_gpd_alignments,49
+gen_marker_gpd_alignment_members,0
+gen_marker_gpd_consensus,50
+gen_marker_atp6_sequences,50
+gen_marker_atp6_alignments,50
+gen_marker_atp6_alignment_members,0
+gen_marker_atp6_consensus,50
+gen_marker_cox1_sequences,50
+gen_marker_cox1_alignments,50
+gen_marker_cox1_alignment_members,0
+gen_marker_cox1_consensus,50
+gen_marker_cox3_sequences,50
+gen_marker_cox3_alignments,50
+gen_marker_cox3_alignment_members,0
+gen_marker_cox3_consensus,50
+gen_marker_nadh_sequences,50
+gen_marker_nadh_alignments,49
+gen_marker_nadh_alignment_members,0
+gen_marker_nadh_consensus,50
+bio_compound_classes,49
+bio_compounds,50
+bio_compound_synonyms,50
+bio_species_compound_occurrences,50
+bio_biosynthetic_gene_clusters,50
+bio_enzymes,50
+bio_protein_enzymes,0
+bio_toxin_amatoxins,50
+bio_toxin_phallotoxins,50
+bio_toxin_orellanines,50
+bio_toxin_gyromitrins,50
+bio_toxin_muscarines,50
+bio_toxin_ibotenic_acids,50
+bio_toxin_psilocybins,50
+bio_toxin_coprines,50
+bio_pigments,50
+bio_antimicrobial_assays,50
+phy_software,48
+phy_substitution_models,47
+phy_trees,0
+phy_tree_inputs,50
+phy_tree_tips,50
+phy_node_supports,0
+phy_divergence_estimates,50
+cul_media_types,47
+cul_media_recipes,50
+cul_strains,49
+cul_growth_experiments,50
+cul_fruiting_protocols,50
+cul_strain_storage_events,50
+pat_host_organism_kingdoms,48
+pat_host_organisms,50
+pat_diseases,50
+pat_disease_associations,50
+pat_clinical_isolates,0
+pat_antifungal_susceptibility,0
+lic_growth_forms,49
+lic_photobiont_groups,50
+lic_lichens,50
+lic_secondary_substances,50
+lic_spot_tests,50
+field_expeditions,50
+field_plots,50
+field_transects,50
+field_weather_logs,50
+field_observations,50
+cur_quality_flag_types,50
+cur_quality_flags,0
+cur_workflow_states,50
+cur_data_sources,50
+cur_provenance,50
+img_image_kinds,50
+img_licenses,47
+img_images,50
+img_image_links,50
+img_image_annotations,50
+ord_agaricales_morphology,55
+ord_agaricales_ecology,55
+ord_agaricales_phenology,55
+ord_agaricales_host_associations,55
+ord_agaricales_substrate_preferences,55
+ord_agaricales_geographic_distribution,55
+ord_agaricales_phylogeny,55
+ord_agaricales_genomics,55
+ord_agaricales_biochemistry,55
+ord_agaricales_cultivation_notes,1
+ord_agaricales_pathogenicity,0
+ord_agaricales_edibility,55
+ord_agaricales_medicinal_uses,55
+ord_agaricales_taxonomic_revisions,55
+ord_agaricales_conservation_status,55
+ord_agaricales_diagnostic_keys,55
+ord_agaricales_type_species_register,55
+ord_agaricales_distribution_grids,55
+ord_agaricales_microclimate_studies,55
+ord_agaricales_dna_barcoding_status,3
+ord_agaricales_spore_print_data,55
+ord_agaricales_mating_systems,55
+ord_agaricales_nutrient_uptake_studies,55
+ord_agaricales_range_maps,55
+ord_agaricales_abundance_estimates,55
+ord_agaricales_toxin_profiles,55
+ord_agaricales_enzyme_activity_assays,55
+ord_agaricales_biocontrol_evaluations,55
+ord_agaricales_regional_checklists,55
+ord_boletales_morphology,55
+ord_boletales_ecology,55
+ord_boletales_phenology,55
+ord_boletales_host_associations,55
+ord_boletales_substrate_preferences,55
+ord_boletales_geographic_distribution,55
+ord_boletales_phylogeny,55
+ord_boletales_genomics,55
+ord_boletales_biochemistry,55
+ord_boletales_cultivation_notes,1
+ord_boletales_pathogenicity,0
+ord_boletales_edibility,55
+ord_boletales_medicinal_uses,55
+ord_boletales_taxonomic_revisions,55
+ord_boletales_conservation_status,55
+ord_boletales_diagnostic_keys,55
+ord_boletales_type_species_register,55
+ord_boletales_distribution_grids,55
+ord_boletales_microclimate_studies,55
+ord_boletales_dna_barcoding_status,0
+ord_boletales_spore_print_data,55
+ord_boletales_mating_systems,55
+ord_boletales_nutrient_uptake_studies,55
+ord_boletales_range_maps,55
+ord_boletales_abundance_estimates,55
+ord_boletales_toxin_profiles,55
+ord_boletales_enzyme_activity_assays,55
+ord_boletales_biocontrol_evaluations,55
+ord_boletales_regional_checklists,55
+ord_russulales_morphology,55
+ord_russulales_ecology,55
+ord_russulales_phenology,55
+ord_russulales_host_associations,55
+ord_russulales_substrate_preferences,55
+ord_russulales_geographic_distribution,55
+ord_russulales_phylogeny,55
+ord_russulales_genomics,55
+ord_russulales_biochemistry,55
+ord_russulales_cultivation_notes,0
+ord_russulales_pathogenicity,2
+ord_russulales_edibility,55
+ord_russulales_medicinal_uses,55
+ord_russulales_taxonomic_revisions,55
+ord_russulales_conservation_status,55
+ord_russulales_diagnostic_keys,55
+ord_russulales_type_species_register,55
+ord_russulales_distribution_grids,55
+ord_russulales_microclimate_studies,55
+ord_russulales_dna_barcoding_status,0
+ord_russulales_spore_print_data,55
+ord_russulales_mating_systems,55
+ord_russulales_nutrient_uptake_studies,55
+ord_russulales_range_maps,55
+ord_russulales_abundance_estimates,55
+ord_russulales_toxin_profiles,55
+ord_russulales_enzyme_activity_assays,55
+ord_russulales_biocontrol_evaluations,55
+ord_russulales_regional_checklists,55
+ord_polyporales_morphology,55
+ord_polyporales_ecology,55
+ord_polyporales_phenology,55
+ord_polyporales_host_associations,55
+ord_polyporales_substrate_preferences,55
+ord_polyporales_geographic_distribution,55
+ord_polyporales_phylogeny,55
+ord_polyporales_genomics,55
+ord_polyporales_biochemistry,55
+ord_polyporales_cultivation_notes,1
+ord_polyporales_pathogenicity,0
+ord_polyporales_edibility,55
+ord_polyporales_medicinal_uses,55
+ord_polyporales_taxonomic_revisions,55
+ord_polyporales_conservation_status,55
+ord_polyporales_diagnostic_keys,55
+ord_polyporales_type_species_register,55
+ord_polyporales_distribution_grids,55
+ord_polyporales_microclimate_studies,55
+ord_polyporales_dna_barcoding_status,0
+ord_polyporales_spore_print_data,55
+ord_polyporales_mating_systems,55
+ord_polyporales_nutrient_uptake_studies,55
+ord_polyporales_range_maps,55
+ord_polyporales_abundance_estimates,55
+ord_polyporales_toxin_profiles,55
+ord_polyporales_enzyme_activity_assays,55
+ord_polyporales_biocontrol_evaluations,55
+ord_polyporales_regional_checklists,55
+ord_thelephorales_morphology,55
+ord_thelephorales_ecology,55
+ord_thelephorales_phenology,55
+ord_thelephorales_host_associations,55
+ord_thelephorales_substrate_preferences,55
+ord_thelephorales_geographic_distribution,55
+ord_thelephorales_phylogeny,55
+ord_thelephorales_genomics,55
+ord_thelephorales_biochemistry,55
+ord_thelephorales_cultivation_notes,0
+ord_thelephorales_pathogenicity,0
+ord_thelephorales_edibility,55
+ord_thelephorales_medicinal_uses,55
+ord_thelephorales_taxonomic_revisions,55
+ord_thelephorales_conservation_status,55
+ord_thelephorales_diagnostic_keys,55
+ord_thelephorales_type_species_register,55
+ord_thelephorales_distribution_grids,55
+ord_thelephorales_microclimate_studies,55
+ord_thelephorales_dna_barcoding_status,0
+ord_thelephorales_spore_print_data,55
+ord_thelephorales_mating_systems,55
+ord_thelephorales_nutrient_uptake_studies,55
+ord_thelephorales_range_maps,55
+ord_thelephorales_abundance_estimates,55
+ord_thelephorales_toxin_profiles,55
+ord_thelephorales_enzyme_activity_assays,55
+ord_thelephorales_biocontrol_evaluations,55
+ord_thelephorales_regional_checklists,55
+ord_cantharellales_morphology,55
+ord_cantharellales_ecology,55
+ord_cantharellales_phenology,55
+ord_cantharellales_host_associations,55
+ord_cantharellales_substrate_preferences,55
+ord_cantharellales_geographic_distribution,55
+ord_cantharellales_phylogeny,55
+ord_cantharellales_genomics,55
+ord_cantharellales_biochemistry,55
+ord_cantharellales_cultivation_notes,0
+ord_cantharellales_pathogenicity,0
+ord_cantharellales_edibility,55
+ord_cantharellales_medicinal_uses,55
+ord_cantharellales_taxonomic_revisions,55
+ord_cantharellales_conservation_status,55
+ord_cantharellales_diagnostic_keys,55
+ord_cantharellales_type_species_register,55
+ord_cantharellales_distribution_grids,55
+ord_cantharellales_microclimate_studies,55
+ord_cantharellales_dna_barcoding_status,1
+ord_cantharellales_spore_print_data,55
+ord_cantharellales_mating_systems,55
+ord_cantharellales_nutrient_uptake_studies,55
+ord_cantharellales_range_maps,55
+ord_cantharellales_abundance_estimates,55
+ord_cantharellales_toxin_profiles,55
+ord_cantharellales_enzyme_activity_assays,55
+ord_cantharellales_biocontrol_evaluations,55
+ord_cantharellales_regional_checklists,55
+ord_hymenochaetales_morphology,55
+ord_hymenochaetales_ecology,55
+ord_hymenochaetales_phenology,55
+ord_hymenochaetales_host_associations,55
+ord_hymenochaetales_substrate_preferences,55
+ord_hymenochaetales_geographic_distribution,55
+ord_hymenochaetales_phylogeny,55
+ord_hymenochaetales_genomics,55
+ord_hymenochaetales_biochemistry,55
+ord_hymenochaetales_cultivation_notes,0
+ord_hymenochaetales_pathogenicity,0
+ord_hymenochaetales_edibility,55
+ord_hymenochaetales_medicinal_uses,55
+ord_hymenochaetales_taxonomic_revisions,55
+ord_hymenochaetales_conservation_status,55
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+ord_microsporidiales_ecology,55
+ord_microsporidiales_phenology,55
+ord_microsporidiales_host_associations,55
+ord_microsporidiales_substrate_preferences,55
+ord_microsporidiales_geographic_distribution,55
+ord_microsporidiales_phylogeny,55
+ord_microsporidiales_genomics,55
+ord_microsporidiales_biochemistry,55
+ord_microsporidiales_cultivation_notes,0
+ord_microsporidiales_pathogenicity,0
+ord_microsporidiales_edibility,55
+ord_microsporidiales_medicinal_uses,55
+ord_microsporidiales_taxonomic_revisions,55
+ord_microsporidiales_conservation_status,55
+ord_microsporidiales_diagnostic_keys,55
+ord_microsporidiales_type_species_register,55
+ord_microsporidiales_distribution_grids,55
+ord_microsporidiales_microclimate_studies,55
+ord_microsporidiales_dna_barcoding_status,0
+ord_microsporidiales_spore_print_data,55
+ord_microsporidiales_mating_systems,55
+ord_microsporidiales_nutrient_uptake_studies,55
+ord_microsporidiales_range_maps,55
+ord_microsporidiales_abundance_estimates,55
+ord_microsporidiales_toxin_profiles,55
+ord_microsporidiales_enzyme_activity_assays,55
+ord_microsporidiales_biocontrol_evaluations,55
+ord_microsporidiales_regional_checklists,55
+tax_species_audit,0
+tax_genera_audit,0
+tax_families_audit,0
+tax_orders_audit,0
+tax_classes_audit,0
+tax_phyla_audit,0
+tax_subspecies_audit,0
+tax_varieties_audit,0
+tax_forms_audit,0
+spc_specimens_audit,0
+spc_collection_events_audit,0
+spc_loans_audit,0
+gen_sequences_audit,0
+gen_assemblies_audit,0
+gen_dna_extracts_audit,0
+phy_trees_audit,0
+bio_compounds_audit,0
+bio_species_compound_occurrences_audit,0
+cul_strains_audit,0
+pat_disease_associations_audit,0
+pat_clinical_isolates_audit,0
+eco_phenology_observations_audit,0
+eco_iucn_assessments_audit,0
+lic_lichens_audit,0
+img_images_audit,0
+field_expeditions_audit,0

mycobase_questions.csv

@@ -0,0 +1,26 @@
+Question,SQL
+"Which species in our database contain amatoxins, and at what
+> concentrations?","SELECT s.scientific_name, c.preferred_name, o.concentration_mg_per_g
+FROM bio_species_compound_occurrences o
+JOIN tax_species s ON s.id = o.species_id
+JOIN bio_compounds c ON c.id = o.compound_id
+JOIN bio_toxin_amatoxins t ON t.compound_id = c.id
+ORDER BY s.scientific_name, c.preferred_name;"
+"Show me ITS sequences with their species and the herbarium voucher
+> they came from.","SELECT s.scientific_name,
+       h.ih_code || ' ' || sp.catalog_number AS voucher,
+       seq.length_bp, seq.gc_content_pct
+FROM gen_sequences seq
+JOIN spc_specimens sp ON sp.id = seq.specimen_id
+JOIN people_herbaria h ON h.id = sp.herbarium_id
+JOIN tax_species s ON s.id = sp.identified_species_id
+WHERE seq.locus = 'its';"
+"Which Agaricales species are classified as deadly, and what is the
+> mean amatoxin concentration reported for each?","SELECT s.scientific_name, e.edibility_class,
+       AVG(o.concentration_mg_per_g) AS mean_amatoxin
+FROM ord_agaricales_edibility e
+JOIN tax_species s ON s.id = e.species_id
+LEFT JOIN bio_species_compound_occurrences o ON o.species_id = s.id
+LEFT JOIN bio_toxin_amatoxins t ON t.compound_id = o.compound_id
+WHERE e.edibility_class = 'deadly'
+GROUP BY s.scientific_name, e.edibility_class;"

mycobase_sqlite_seed_data.sql

@@ -0,0 +1,359 @@
+-- ===================================================================
+-- 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;

train.json

@@ -0,0 +1,20 @@
+[
+  {
+    "question": "Which species in our database contain amatoxins, and at what\n> concentrations?",
+    "query": "SELECT s.scientific_name, c.preferred_name, o.concentration_mg_per_g\nFROM bio_species_compound_occurrences o\nJOIN tax_species s ON s.id = o.species_id\nJOIN bio_compounds c ON c.id = o.compound_id\nJOIN bio_toxin_amatoxins t ON t.compound_id = c.id\nORDER BY s.scientific_name, c.preferred_name;",
+    "db_id": "mycobase",
+    "evidence": ""
+  },
+  {
+    "question": "Show me ITS sequences with their species and the herbarium voucher\n> they came from.",
+    "query": "SELECT s.scientific_name,\n       h.ih_code || ' ' || sp.catalog_number AS voucher,\n       seq.length_bp, seq.gc_content_pct\nFROM gen_sequences seq\nJOIN spc_specimens sp ON sp.id = seq.specimen_id\nJOIN people_herbaria h ON h.id = sp.herbarium_id\nJOIN tax_species s ON s.id = sp.identified_species_id\nWHERE seq.locus = 'its';",
+    "db_id": "mycobase",
+    "evidence": ""
+  },
+  {
+    "question": "Which Agaricales species are classified as deadly, and what is the\n> mean amatoxin concentration reported for each?",
+    "query": "SELECT s.scientific_name, e.edibility_class,\n       AVG(o.concentration_mg_per_g) AS mean_amatoxin\nFROM ord_agaricales_edibility e\nJOIN tax_species s ON s.id = e.species_id\nLEFT JOIN bio_species_compound_occurrences o ON o.species_id = s.id\nLEFT JOIN bio_toxin_amatoxins t ON t.compound_id = o.compound_id\nWHERE e.edibility_class = 'deadly'\nGROUP BY s.scientific_name, e.edibility_class;",
+    "db_id": "mycobase",
+    "evidence": ""
+  }
+]