license: cc
tags:
- protein
- biology
- botany
pretty_name: GreenBeing
configs:
- config_name: default
data_files:
- split: pretraining
path: proteins_pretraining.csv
- split: finetuning
path: proteins_finetuning.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.
XML source from https://www.uniprot.org/help/downloads
CoLab notebook: https://colab.research.google.com/drive/1M6sO0Ws6i5z9VUXIXopiOqo1OkQ7K-1g?usp=sharing
Pretraining set
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 set:
- 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 set
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 reviewed set are from rice and related species, a fifth are from Papilionoideae/Faboideae, and seven taxa have less than 1%.
Research set (TODO)
Formatted like the finetuning set, but with proteins from quinoa and amaranth.
Limitations and Safety Notes
Proteins and review status on UniProt are from late March 2024.
You should at least pretrain on more than Oryza sativa, because its reviewed proteins are probably some of the most common/important.
The reviewed sequences are often similar to unreviewed sequences from related species and accessions, and are not suitable to 'predict' protein completion.
Species include inedible wild relatives.
Some people have allergic reactions to wheat/gluten, nightshades, maize, and other crops.
Chili peppers can be painfully spicy.