metadata.json

{
  "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)"
  }
}