---
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
configs:
- config_name: tax_species
  data_files: "data/tax_species.csv"
- config_name: spc_specimens
  data_files: "data/spc_specimens.csv"
- config_name: lit_publications
  data_files: "data/lit_publications.csv"
- config_name: people_persons
  data_files: "data/people_persons.csv"
- config_name: gen_sequences
  data_files: "data/gen_sequences.csv"
- config_name: benchmark_summary
  data_files: "mycobase_benchmark_summary.csv"
---

# 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.
- `evaluation_questions.json`: Natural Language to SQL query pairs for training/evaluation (renamed from train.json).
- `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