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README.md
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---
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license: mit
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---
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license: mit
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task_categories:
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- text-classification
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tags:
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- biology
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size_categories:
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- 1K<n<10K
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---
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# greenbeing-binary
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This is a binary classification version of the finetuning/evaluation datasets introduced in
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the freeform text annotations of the [greenbeing-proteins](https://huggingface.co/datasets/monsoon-nlp/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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## Tasks
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The "query" field currently contains 18 possible labels from the annotation, and the "label" field is the binary class (0 = No, 1 = Yes)
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### Subcellular Locations
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```
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'cell membrane', # negatives cannot include: cell surface, cell wall
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'endoplasmic reticulum',
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'plastid',
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'chloroplast',
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'vacuole',
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'nucleus',
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'microsome',
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'cytoplasm',
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'extracellular space',
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'mitochondrion',
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'golgi',
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'endosome membrane',
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'cytoskeleton',
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'chromosome',
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'nucleolus',
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'spindle',
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'extracellular matrix',
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'centromere',
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```
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All positives are included (between 4 and 673), and ~100 randomly selected annotated proteins without this location are included in negatives.
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Dataset notebook: https://colab.research.google.com/drive/1QQPjXpqBrd75vP8UbPmZqo-LlcOSyzZu?usp=sharing
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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, and an amino acid sequence.
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A gene name may match multiple entries on UniProt from different accessions.
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## Evaluation split
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**Reviewed proteins (Swiss-Prot)** from other genera (avocado, carrot, cassava, lychee, prunus (i.e. peaches, cherries, plums)).
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Each row contains a gene name, species or subspecies, and an amino acid sequence.
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A gene name may match multiple entries on UniProt from different accessions.
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