| | --- |
| | 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 |
