license: cc
tags:
- protein
- biology
- botany
pretty_name: GreenBeing
configs:
- config_name: pretraining
data_files:
- split: pretraining
path: proteins_pretraining.csv
- config_name: finetuning
data_files:
- split: finetuning
path: proteins_finetuning.csv
- config_name: evaluation
data_files:
- split: evaluation
path: proteins_evaluation.csv
- config_name: research
data_files:
- split: research
path: proteins_research.csv
GreenBeing Proteins dataset
Proteins from UniProtKB (knowledge base), from select food crops and related species.
Amino acid sequences use IUPAC-IUB codes where letters A-Z map to amino acids.
Usage (due to different schema on splits):
load_dataset("monsoon-nlp/greenbeing-proteins", "pretraining", split="pretraining")
XML source from https://www.uniprot.org/help/downloads
CoLab notebook: https://colab.research.google.com/drive/1M6sO0Ws6i5z9VUXIXopiOqo1OkQ7K-1g?usp=sharing
Pretraining split
Amino acid sequences for unreviewed proteins (TrEMBL)
Each row contains a species or subspecies name (for filtering), and the amino acid sequence of a protein. Large proteins are split into a new row every 8,000 letters.
Share of taxa
In the pretraining split:
- 31% Papilionoideae/Faboideae (soybeans, peas, pulses, peanuts)
- 19% Triticeae (wheat, barley, rye, and relatives)
- 17% Oryzeae (rice, wild rice, and relatives)
- 12% Paniceae (most millets)
- 6% Solanum (potatoes, tomatoes, other nightshades, etc.)
- 5% Zea (corn/maize)
- 2% Sorghum
- 2% Lactuca sativa (lettuce)
- 2% Capsicum (chili peppers)
- 2% Cucurbita (squash, pumpkins)
- 0.8% Spinacia
- 0.7% Asparagus
- 0.2% Beta vulgaris (beet)
- 0.1% Bambusa (includes edible bamboo shoots)
Finetuning split
Reviewed proteins (Swiss-Prot) from above taxa. Each row contains a gene name, species or subspecies, an amino acid sequence, and comments / annotations available in UniProt.
A gene name may match multiple entries on UniProt from different accessions.
Annotations may be empty, or may include information such as:
- likely function, written in English
- location inside of cell (e.g. "Subcellular locations: Vacuole")
- locations in the plant (e.g. "Expressed in roots, stems")
Removed PubMed reference numbers to avoid training models to hallucinate PubMed references.
In the current state of plant genomics research, about half of the finetuning split are from rice and related species, a fifth are from Papilionoideae/Faboideae, and seven taxa have less than 1% each.
Evaluation split
Reviewed proteins (Swiss-Prot) from other genera (avocado, carrot, cassava, lychee, prunus (i.e. peaches, cherries, plums)). Each row contains a gene name, species or subspecies, an amino acid sequence, and comments / annotations available in UniProt.
A gene name may match multiple entries on UniProt from different accessions.
Annotations may be empty, or may include information such as:
- likely function, written in English
- location inside of cell (e.g. "Subcellular locations: Vacuole")
- locations in the plant (e.g. "Expressed in roots, stems")
Removed PubMed reference numbers to avoid training models to hallucinate PubMed references.
Research split
Proteins from quinoa (~99%), cañihua, and the three species of amaranth which are currently grown for grain.
Columns contain UniProt/TrEMBL gene names, species, and the amino acid sequence. Large proteins are split into a new row every 8,000 letters.
Limitations and Safety Notes
Proteins and review status on UniProt are from March 29, 2024.
You should at least pretrain on more than Oryza sativa, because its reviewed proteins are probably some of the most common/important.
Understanding reviewed/unreviewed proteins: https://www.uniprot.org/help/uniprotkb_sections
The reviewed sequences are often similar to unreviewed sequences from related species and accessions, and are not suitable to test predicting/infilling/completion.
Species include inedible wild relatives.
Some people have allergic reactions to wheat/gluten, nightshades, maize, lychee, and other crops.
Chili peppers can be painfully spicy.