Datasets:

titodamiani
/

AngioNCS

License:

Dataset Viewer

The dataset viewer is not available for this subset.

Cannot get the split names for the config 'default' of the dataset.

Exception:    SplitsNotFoundError
Message:      The split names could not be parsed from the dataset config.
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 289, in get_dataset_config_info
                  for split_generator in builder._split_generators(
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 83, in _split_generators
                  raise ValueError(
              ValueError: The TAR archives of the dataset should be in WebDataset format, but the files in the archive don't share the same prefix or the same types.
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/split_names.py", line 65, in compute_split_names_from_streaming_response
                  for split in get_dataset_split_names(
                               ^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 343, in get_dataset_split_names
                  info = get_dataset_config_info(
                         ^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 294, in get_dataset_config_info
                  raise SplitsNotFoundError("The split names could not be parsed from the dataset config.") from err
              datasets.inspect.SplitsNotFoundError: The split names could not be parsed from the dataset config.

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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

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