| { |
| "dataset_name": "SourceData-NEL", |
| "version": "1.0.0", |
| "description": "Named Entity Linking dataset from SourceData with UniProt ground truth", |
| "statistics": { |
| "total_records": 16532, |
| "splits": { |
| "train": { |
| "count": 14880, |
| "file": "data/nel_dataset_role_filtered/train.jsonl" |
| }, |
| "val": { |
| "count": 825, |
| "file": "data/nel_dataset_role_filtered/val.jsonl" |
| }, |
| "test": { |
| "count": 827, |
| "file": "data/nel_dataset_role_filtered/test.jsonl" |
| } |
| } |
| }, |
| "splits": { |
| "train": 0.9, |
| "val": 0.05, |
| "test": 0.05 |
| }, |
| "schema": { |
| "pmid": "PubMed ID", |
| "doi": "Digital Object Identifier", |
| "title": "Paper title", |
| "abstract": "Paper abstract", |
| "year": "Publication year", |
| "fig_label": "Figure label (e.g., 'Figure 1')", |
| "caption": "Figure caption text", |
| "fig_href": "Figure URL", |
| "entities": "List of gene/protein entities mentioned in caption", |
| "entities[].text": "Entity mention text", |
| "entities[].type": "Entity type (geneprod for NER compatibility)", |
| "entities[].original_type": "Original type from SourceData (gene or protein)", |
| "entities[].role": "Biological role", |
| "entities[].ext_tax_names": "Organism taxonomy name", |
| "entities[].ext_tax_ids": "Taxonomy IDs", |
| "entities[].uniprot_ids": "Ground truth UniProt accessions (list, empty if unmapped)", |
| "entities[].ncbi_gene_id": "NCBI Gene ID (if original_type=gene)", |
| "entities[].mapping_source": "Source of UniProt ID (direct/ncbi_gene/unmapped)", |
| "entities[].mapping_status": "Mapping status (mapped/unmapped)" |
| } |
| } |
