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Datasets:
EMBO
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soda-nel

Tasks:
Text Classification
Modalities:
Text
Formats:
parquet
Languages:
English
Size:
10K - 100K
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Tags:
biology
proteins
genes
uniprot
named-entity-linking
biomedical
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metadata
license: mit
task_categories:
  - named-entity-recognition
  - named-entity-linking
  - text-classification
language:
  - en
tags:
  - biology
  - proteins
  - genes
  - uniprot
  - named-entity-linking
  - biomedical
  - life-sciences
size_categories:
  - 10K<n<100K

SODA-SPROUT: Role-Filtered Named Entity Linking Dataset

Dataset Description

This dataset is an improved version of the SODA-SPROUT NEL dataset, specifically filtered to include only the most relevant biological entities for Named Entity Linking tasks. The dataset focuses on proteins and genes with roles of 'assayed' and 'intervention', which represent the core biological entities that are actually measured or manipulated in scientific experiments.

Key Improvements

  • Role Filtering: Only includes entities with roles 'assayed' (104,286 entities) and 'intervention' (80,127 entities)
  • Higher Quality: Removes less relevant entities like 'reporter', 'component', 'normalizing', and 'experiment' roles
  • Better NEL Performance: Focuses on the most important biological entities for linking tasks
  • Reduced Noise: 16,532 figure-level records (vs. 21,000+ in unfiltered version)

Dataset Structure

Statistics

  • Total Records: 16,532 figure-level records
  • Training Set: 14,880 records (90%)
  • Validation Set: 825 records (5%)
  • Test Set: 827 records (5%)
  • Total Entities: 184,413 (104,286 assayed + 80,127 intervention)
  • Unique Papers: 3,101 papers

Data Format

Each record contains:

  • Paper Context: PMID, DOI, title, abstract, year
  • Figure Context: Figure label, caption, figure URL
  • Entities: List of gene/protein entities with:
    • text: Entity mention text
    • type: "geneprod" (for NER compatibility)
    • original_type: "gene" or "protein" (from SourceData)
    • role: "assayed" or "intervention"
    • ext_tax_names: Organism taxonomy name
    • uniprot_ids: Ground truth UniProt accessions
    • mapping_status: "mapped" or "unmapped"

Usage 

from datasets import load_dataset

# Load the dataset
dataset = load_dataset("EMBO/soda-nel")

# Access splits
train_data = dataset["train"]
val_data = dataset["validation"] 
test_data = dataset["test"]

# Example record
record = train_data[0]
print(f"Paper: {record['title']}")
print(f"Figure: {record['fig_label']}")
print(f"Caption: {record['caption']}")
print(f"Entities: {len(record['entities'])}")

Role Definitions

  • Assayed: Proteins/genes that were actually measured, quantified, or tested in the experiment
  • Intervention: Proteins/genes that were manipulated, targeted, or used as experimental interventions

Data Sources

Citation

If you use this dataset, please cite both the original SourceData paper and this improved version:

@article{source_data_2023,
  title={SourceData: A platform for the large-scale curation of unstructured data from the scientific literature},
  author={...},
  journal={...},
  year={2023},
  url={https://arxiv.org/abs/2310.20440}
}

License

This dataset is released under the MIT License. The underlying SourceData is available under its original license.

Updates

  • v1.1.0: Added role filtering for 'assayed' and 'intervention' entities only
  • v1.0.0: Initial release with all entity roles