README.md

metadata

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 file in the corresponding GitHub repository, where all code an scripts are hosted.

Dataset structure

This dataset follows the 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 (MGF file) and associated metadata (CSV file) from version 1.3.1, downloaded on 3.12.2025
• The transcriptomes folders contains assembled transcriptomes (FASTA format) from the 1K Plant Transcriptomes 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
• The fastmasst folder contains the output of plantMASST batch search (version 1.8.0) 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 and classified with GBIF Backbone Taxonomy
• The summary.csv file summarized various datasets (e.g., Wikidata reports, MS/MS matches) mapped onto the genus-level Angiosperm ToL