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JNLPBA

archive 2025-07-28

JNLPBA is a biomedical dataset that comes from the GENIA version 3.02 corpus (Kim et al., 2003). It was created with a controlled search on MEDLINE. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. 36 terminal classes were used to annotate the GENIA corpus.

HomepageBenchmarksPapers JSON

Benchmarks archive 2025-07-28

All 2 leaderboards 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)PaperCode
Named Entity Recognition (NER) JNLPBA KeBioLM F1 82.0 Improving Biomedical Pretrained Language Models with Knowledge GanjinZero/KeBioLM 17 Compare
Relation Extraction JNLPBA SciBERT (SciVocab) F1 76.09 SciBERT: A Pretrained Language Model for Scientific Text allenai/scibert +5 1 Compare

Papers archive 2025-07-28

12 shown of 12 papers 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 20. The Syntology column is from Syntology's graph (read 2026-09-24), stated per sample; it is not part of any archive number.

DateSamples run Syntology
On the Effectiveness of Compact Biomedical Transformers 1 4 7 Sep 2022 not harvested
Optimizing Bi-Encoder for Named Entity Recognition via Contrastive Learning 1 1 30 Aug 2022 ran 4 of 4 samples (0 unverified)
MINER: Improving Out-of-Vocabulary Named Entity Recognition from an Information Theoretic Perspective 2 1 9 Apr 2022 ran 0 of 2 samples (2 unverified)
LinkBERT: Pretraining Language Models with Document Links 1 1 29 Mar 2022 ran 0 of 14 samples (14 unverified)
SciFive: a text-to-text transformer model for biomedical literature 1 1 28 May 2021 ran 0 of 5 samples (5 unverified)
Improving Biomedical Pretrained Language Models with Knowledge 1 1 21 Apr 2021 not harvested
Improving Biomedical Named Entity Recognition with Syntactic Information 1 1 25 Nov 2020 not harvested
Biomedical Named Entity Recognition at Scale 1 2 12 Nov 2020 not harvested
Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing 2 1 31 Jul 2020 not harvested
BioFLAIR: Pretrained Pooled Contextualized Embeddings for Biomedical Sequence Labeling Tasks 1 1 13 Aug 2019 not harvested
SciBERT: A Pretrained Language Model for Scientific Text 6 2 26 Mar 2019 not harvested
BioBERT: a pre-trained biomedical language representation model for biomedical text mining 19 1 25 Jan 2019 ran 4 of 25 samples (21 unverified; 1 pointer-only for licence)

Dataset loaders archive 2025-07-28

hanaeFSDM/BioNERtf

1 loader as listed in the archive; links are outbound and not re-checked here.

Tasks archive 2025-07-28

Named Entity Recognition (NER)Relation ExtractionMedical Named Entity Recognition

License archive 2025-07-28

No licence recorded in the archive. Absence here is not a statement about the dataset's terms.

Modalities archive 2025-07-28

Texts

Languages archive 2025-07-28

No language tagged.

Variants archive 2025-07-28

  • JNLPBA

1 variant name, as the archive lists them.

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