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BC5CDR (BioCreative V CDR corpus)

Introduced in BioCreative V CDR task corpus: a resource for chemical disease relation extraction1 Jan 2016 archive 2025-07-28

BC5CDR corpus consists of 1500 PubMed articles with 4409 annotated chemicals, 5818 diseases and 3116 chemical-disease interactions.

Source: https://www.ncbi.nlm.nih.gov/research/bionlp/Data/ Image Source: https://arxiv.org/pdf/1805.10586.pdf

HomepageBenchmarksPapers JSON

Benchmarks archive 2025-07-28

All 4 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) BC5CDR BINDER F1 91.9 Optimizing Bi-Encoder for Named Entity Recognition via... microsoft/binder 16 Compare
Named Entity Recognition (NER) BC5CDR-chemical Spark NLP F1 94.88 Biomedical Named Entity Recognition at Scale JohnSnowLabs/spark-nlp-workshop 13 Compare
Named Entity Recognition (NER) BC5CDR-disease BioMegatron F1 88.5 BioMegatron: Larger Biomedical Domain Language Model NVIDIA/NeMo 10 Compare
UIE BC5CDR KnowCoder-7b-IE F1 score 89.3 KnowCoder: Coding Structured Knowledge into LLMs for... ICT-GoKnow/KnowCoder 1 Compare

Papers archive 2025-07-28

22 shown of 22 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 191. 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
KnowCoder: Coding Structured Knowledge into LLMs for Universal Information Extraction 1 1 12 Mar 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)
Enhancing Label Consistency on Document-level Named Entity Recognition 1 1 24 Oct 2022 not harvested
On the Effectiveness of Compact Biomedical Transformers 1 8 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)
Accurate clinical and biomedical Named entity recognition at scale 1 1 19 Jul 2022 not harvested
Hero-Gang Neural Model For Named Entity Recognition 1 2 15 May 2022 not harvested
LinkBERT: Pretraining Language Models with Document Links 1 3 29 Mar 2022 ran 0 of 14 samples (14 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 2 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 2 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 3 12 Nov 2020 not harvested
BioMegatron: Larger Biomedical Domain Language Model 1 2 12 Oct 2020 not harvested
Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets 4 2 13 Jun 2019 ran 0 of 2 samples (2 unverified)
An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition 1 1 15 Apr 2019 not harvested
SciBERT: A Pretrained Language Model for Scientific Text 6 2 26 Mar 2019 not harvested
CollaboNet: collaboration of deep neural networks for biomedical named entity recognition 2 1 21 Sep 2018 not harvested

Dataset loaders archive 2025-07-28

sq1balaji/EasyOCR-ChatBottfpytorch

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

Tasks archive 2025-07-28

Named Entity Recognition (NER)UIEWeakly-Supervised Named Entity Recognition

License archive 2025-07-28

Custom

Modalities archive 2025-07-28

Texts

Languages archive 2025-07-28

English

Variants archive 2025-07-28

  • BC5CDR
  • BC5CDR-disease
  • BC5CDR-chemical

3 variant names, as the archive lists them.

Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections