The chemotaxonomic map of labdane diterpenoids in Acanthaceae

This repository contains the code for the analysis of labdane diterpenoids in the Acanthaceae profiling project. The analysis includes feature filtering, annotation merging, deduplication, distribution analysis of andrographolide, and chemotaxonomic analysis. The results are generated in the output/ directory.

Repository Structure

├── data/                          # Raw and input data
│   ├── positive_mode/             # Positive-mode MS features & library IDs
│   ├── negative_mode/             # Negative-mode MS features & library IDs
│   ├── figures/                   # Figures for the manuscript
│   ├── kg/                        # Literature data
│   ├── npclassifier_cache.json    # Cached NPClassifier results
│   ├── spectra_metadata.tsv.gz      # Spectra to chemical names/smiles mappings
│   └── metadata.tsv               # Sample metadata with annotations  
├── notebooks/                     # Analysis notebooks (run in order)
│   ├── 1_filtering_neg.ipynb      # Feature filtering – negative mode
│   ├── 1_filtering_pos.ipynb      # Feature filtering – positive mode
│   ├── 2_adding_annotations_from_ometa.ipynb  # Merge metadata annotations
│   ├── 3_feature_deduplication.ipynb          # Deduplicate features
│   ├── 4_andrographolide_distributions.ipynb  # Andrographolide distribution analysis
│   └── 5_chemotaxonomy.ipynb      # Chemotaxonomic analysis
├── output/                        # Output folder for intermediary and final results
└── pyproject.toml                 # Project & dependency configuration

Citation

Domingo-Fernández, D., Slack, P., Bayless, A., Saifi, I., Preto, A., Wen, W., Chisowa, T., DeBloois, E., Wee, D., Colluru, V., Misra, B., and Katz, A. (2026). The chemotaxonomic map of labdane diterpenoids in Acanthaceae. Journal of Natural Products. 10.1021/acs.jnatprod.6c00498