Datasets › The EMBO SourceData-NLP dataset
The EMBO SourceData-NLP dataset (The SourceData-NLP dataset: integrating curation into scientific publishing for training large language models)
We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement.
Benchmarks archive 2025-07-28
All 1 leaderboard whose dataset resolves to this page shown (sort by any header). "First row" is the archive's own first row at snapshot, in the archive's row order; nothing here re-ranks and metric direction is not asserted.
| First row (archive order) | Paper | Code | ||||
|---|---|---|---|---|---|---|
| NER | The EMBO SourceData-NLP dataset | BioLinkBERT-large F1 Micro 84.7 | Integrating curation into scientific publishing to train... | source-data/soda-data | 1 | Compare |
Papers archive 2025-07-28
1 shown of 1 paper with a leaderboard row on this dataset's benchmarks, newest first. The archive's own "papers using this dataset" list was never published, so this is the benchmark-backed subset; the archive's count for this dataset is 1. The Syntology column is from Syntology's graph (read 2026-09-24), stated per sample; it is not part of any archive number.
| Date | Samples run Syntology | |||
|---|---|---|---|---|
| Integrating curation into scientific publishing to train AI models | 1 | 1 | 31 Oct 2023 | not harvested |
Dataset loaders archive 2025-07-28
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Tasks archive 2025-07-28
License archive 2025-07-28
CC 4.0
Modalities archive 2025-07-28
Languages archive 2025-07-28
Variants archive 2025-07-28
- The EMBO SourceData-NLP dataset
1 variant name, as the archive lists them.
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