| --- |
| 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 |
| |
