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Datasets › NCBI Disease

NCBI Disease

Introduced in NCBI disease corpus: A resource for disease name recognition and concept normalization1 Jan 2014 archive 2025-07-28

The NCBI Disease corpus consists of 793 PubMed abstracts, which are separated into training (593), development (100) and test (100) subsets. The NCBI Disease corpus is annotated with disease mentions, using concept identifiers from either MeSH or OMIM.

Source: A Neural Multi-Task Learning Framework to Jointly Model Medical Named Entity Recognition and Normalization

HomepageBenchmarksPapers JSON

Benchmarks archive 2025-07-28

All 3 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) NCBI-disease BioBERT F1 89.71 BioBERT: a pre-trained biomedical language... dmis-lab/biobert +18 26 Compare
Named Entity Recognition (NER) NCBI Disease UniNER-7B F1 86.96 UniversalNER: Targeted Distillation from Large Language... universal-ner/universal-ner +1 1 Compare
UIE ncbi_disease KnowCoder-7b-IE F1 score 83.8 KnowCoder: Coding Structured Knowledge into LLMs for... ICT-GoKnow/KnowCoder 1 Compare

Papers archive 2025-07-28

23 shown of 23 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 154. 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
Evaluation of large language model performance on the Biomedical Language Understanding and Reasoning Benchmark 0 1 17 May 2024 not harvested
KnowCoder: Coding Structured Knowledge into LLMs for Universal Information Extraction 1 1 12 Mar 2024 not harvested
NuNER: Entity Recognition Encoder Pre-training via LLM-Annotated Data 1 1 23 Feb 2024 not harvested
GoLLIE: Annotation Guidelines improve Zero-Shot Information-Extraction 1 1 5 Oct 2023 ran 18 of 25 samples (7 unverified)
UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition 2 1 7 Aug 2023 ran 5 of 12 samples (7 unverified)
Comparing and combining some popular NER approaches on Biomedical tasks 1 1 30 May 2023 not harvested
On the Effectiveness of Compact Biomedical Transformers 1 4 7 Sep 2022 not harvested
LinkBERT: Pretraining Language Models with Document Links 1 1 29 Mar 2022 ran 0 of 14 samples (14 unverified)
BERN2: an advanced neural biomedical named entity recognition and normalization tool 1 1 6 Jan 2022 ran 2 of 2 samples (0 unverified)
Focusing on Potential Named Entities During Active Label Acquisition 1 1 6 Nov 2021 not harvested
SciFive: a text-to-text transformer model for biomedical literature 1 1 28 May 2021 ran 0 of 5 samples (5 unverified)
Improving Named Entity Recognition by External Context Retrieving and Cooperative Learning 3 1 8 May 2021 ran 0 of 4 samples (4 unverified)
Improving Biomedical Pretrained Language Models with Knowledge 1 1 21 Apr 2021 not harvested
ELECTRAMed: a new pre-trained language representation model for biomedical NLP 2 1 19 Apr 2021 not harvested
A Robust and Domain-Adaptive Approach for Low-Resource Named Entity Recognition 1 1 2 Jan 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
BioMegatron: Larger Biomedical Domain Language Model 1 1 12 Oct 2020 not harvested
Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing 2 1 31 Jul 2020 not harvested
Learning A Unified Named Entity Tagger From Multiple Partially Annotated Corpora For Efficient Adaptation 1 1 25 Sep 2019 not harvested
A Neural Named Entity Recognition and Multi-Type Normalization Tool for Biomedical Text Mining 1 1 4 Jun 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

huggingface.co/datasets/ncbi/ncbi_diseasehuggingface/datasetstfpytorchjax
huggingface.co/datasets/scillm/ncbi_diseasehuggingface/datasetstfpytorchjax
huggingface.co/datasets/ncbi_diseasehuggingface/datasetstfpytorchjax

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

Tasks archive 2025-07-28

Named Entity Recognition (NER)UIENamed Entity Recognition

License archive 2025-07-28

Unknown

Modalities archive 2025-07-28

Texts

Languages archive 2025-07-28

No language tagged.

Variants archive 2025-07-28

  • NCBI-disease
  • NCBI Disease
  • ncbi_disease

3 variant names, as the archive lists them.

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