---
license: mit
---

This HuggingFace dataset hosts all raw and processed data related to the manuscript **“Norcoclaurine synthases are widespread among angiosperms”** (DOI: *add here*), as they are too large for GitHub. To download the dataset and reproduce the data analysis, please follow the instructions provided in the [README.md](https://github.com/titodamiani/AngioNCS/blob/master/README.md
) file in the corresponding GitHub [repository](https://github.com/titodamiani/AngioNCS), where all code an scripts are hosted.

## Dataset structure
This dataset follows the [Cookiecutter Data Science](https://drivendata.github.io/cookiecutter-data-science/) and is structured as follows:

```
AngioNCS/
├── raw
│   ├── msgym                   # MassSpecGym spectra and metadata
│   └── transcriptomes          # Assembled 1K transcriptomes
├── processed                   
│   ├── ref_ms2.mgf             # Reference BIA spectra from MassSpecGym
│   ├── ref_ms2.csv             # MassSpecGym metadata
│   ├── bia_reports.csv         # Wikidata BIA reports
│   ├── pmasst_clean.csv        # Cleaned plantMASST metadata
│   ├── pmasst_matches.csv      # Aggreagated plantMASST matches
│   └── summary.csv             # Summary dataset for genus-level Angiosperm ToL
├── interim
│   ├── gnverifier              # GNVerifier results
│   └── gbif                    # GBIF Backbone Taxonomy results
├── external
│   ├── fastmasst               # Output from batch plantMASST search
│   ├── trees                   # Phylogenetic trees
│   ├── 1k_transcriptomes.xlsx  # 1K transcriptomes metadata
│   └── plantmasst.tsv          # plantMASST files inventory
└── README.md
```
***Notes*** 
- The `msgym` folder contains MassSpecGym [spectra](https://huggingface.co/datasets/roman-bushuiev/MassSpecGym/blob/main/data/MassSpecGym.tsv) (MGF file) and associated [metadata](https://huggingface.co/datasets/roman-bushuiev/MassSpecGym/blob/main/data/MassSpecGym.tsv) (CSV file) from [version 1.3.1](https://github.com/pluskal-lab/MassSpecGym/releases/tag/v1.3.1), downloaded on 3.12.2025
- The `transcriptomes` folders contains assembled transcriptomes (FASTA format) from the [1K Plant Transcriptomes](https://doi.org/10.1038/s41586-019-1693-2) project, downloaded on [dd.mm.yyyy]
- The `pmasst_clean.csv` file is the plantMASST metadata (`plantmasst.tsv`, downloaded on 22.11.2024) removed of Blank and QC datafiles, and including taxonomic names resolved with [Global Names Verifier](https://verifier.globalnames.org/)
- The `fastmasst` folder contains the output of plantMASST batch search ([version 1.8.0](https://github.com/robinschmid/microbe_masst/releases/tag/v1.8.0)) performed on 3.12.2025 using `ref_ms2.mgf` as input. All PlantMASST output files (i.e., `*_plant.tsv`) are aggregated in `processed/pmasst_matches.csv`.
- The `trees` folder contains phylogenetic trees downloaded from https://zenodo.org/records/10778207
- The `bia_reports.csv` file contains Wikidata reports of BIAs, and includes taxonomic names resolved with [Global Names Verifier](https://verifier.globalnames.org/) and classified with [GBIF Backbone Taxonomy](https://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c)
- The `summary.csv` file summarized various datasets (e.g., Wikidata reports, MS/MS matches) mapped onto the genus-level Angiosperm ToL