Species Trait Data Compilation

This project automates the retrieval and compilation of species-specific biological trait data by integrating biodiversity APIs with large language models. It is designed to scale from focused case studies to generalized, cross-species analyses.

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1. Frog Analysis

The first phase of this project demonstrates a deep dive into amphibians (frogs) as a proof of concept.

• Uses multiple APIs to collect ecological and biological information:
  • AmphibiaWeb: morphology and reproductive traits (snout–vent length, clutch size, egg diameter)
  • IUCN Red List: elevation ranges and habitat categories
  • World Bank CCKP: temperature and rainfall statistics
• Automates retrieval of structured (API) and semi-structured (XML parsed via GPT-4o) data
• Compiles outputs into a clean CSV/Excel dataset with traits like morphology, reproduction, climate, and altitude

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2. Generalized Data Pipeline

The system then expands into a general-purpose trait extraction pipeline.

• Uses Europe PMC / PubMed Central (PMC) to query scientific literature
• Retrieves PDFs, parses them, and applies LLM-based extraction prompts to pull out traits such as diet, size, habitat, or environmental associations
• Works for any list of species and any set of traits, driven by an Excel file and trait description mapping
• Provides a UI for easy use, supporting batch processing across taxa

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How to Use

1. Run the GUI script:

   python3 Data-Compilation-Model/02_generic_data_compilation/scripts/gui.py

2. In the popup window:

   • Upload your Excel file: first column = species, remaining columns = traits.
   • Upload your trait descriptions text file: UTF-16 encoded; each line in the format trait: description.

3. Start extraction:

   • Click Start Data Extraction.
   • The system will query APIs, fetch papers, and extract trait data.
   • Results will be saved to: Data-Compilation-Model/02_generic_data_compilation/results/