license: mit
task_categories:
- text-classification
tags:
- biology
size_categories:
- 1K<n<10K
pretty_name: GreenBeing Binary
configs:
- config_name: binaryclass
data_files:
- split: finetuning
path: proteins_finetuning.csv
- split: evaluation
path: proteins_evaluation.csv
greenbeing-binary
This is a binary classification version of the finetuning/evaluation datasets introduced in the freeform text annotations of the 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.
Tasks
The "query" field currently contains 18 possible labels from the annotation, and the "label" field is the binary class (0 = No, 1 = Yes)
Subcellular Locations
'cell membrane', # negatives cannot include: cell surface, cell wall
'endoplasmic reticulum',
'plastid',
'chloroplast',
'vacuole',
'nucleus',
'microsome',
'cytoplasm',
'extracellular space',
'mitochondrion',
'golgi',
'endosome membrane',
'cytoskeleton',
'chromosome',
'nucleolus',
'spindle',
'extracellular matrix',
'centromere',
All positives are included (between 4 and 673), and ~100 randomly selected annotated proteins without this location are included in negatives.
Dataset builder notebook: https://colab.research.google.com/drive/1QQPjXpqBrd75vP8UbPmZqo-LlcOSyzZu?usp=sharing
Example using a protein embeddings model and SciKit-Learn to build a classifier for "chloroplast" proteins: https://colab.research.google.com/drive/1MCTn8f3oeIKpB6n_8mPumet3ukm7GD8a?usp=sharing
Finetuning split
Reviewed proteins (Swiss-Prot) from above taxa. Each row contains a gene name, species or subspecies, and an amino acid sequence.
A gene name may match multiple entries on UniProt from different accessions.
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, and an amino acid sequence.
A gene name may match multiple entries on UniProt from different accessions.