Update README.md

README.md

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 ---
 license: cc
+tags:
+- protein
+- biology
+- botany
+pretty_name: GreenBeing
 ---
+
+# GreenBeing Proteins dataset
+
+Proteins from UniProtKB (knowledge base), which are from food crops and related species.
+
+Amino acid sequences use [IUPAC-IUB codes](https://en.wikipedia.org/wiki/FASTA_format#Sequence_representation) 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 (TODO)
+
+Amino acid sequences for **unreviewed proteins (TrEMBL)**
+
+Each row contains a species or subspecies name (for filtering), and the amino acid sequence.
+
+### 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.<br/>
+Some people have allergic reactions to wheat/gluten, nightshades, maize, and other crops.<br/>
+Chili peppers can be painfully spicy.