EMBO/soda-nel

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

• Source Dataset: EMBO/SourceData
• Original Paper: SourceData: A platform for the large-scale curation of unstructured data from the scientific literature
• UniProt Mapping: NCBI Gene IDs mapped to UniProt accessions via UniProt REST API

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