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