# NEREL-BIO: A Dataset of Biomedical Abstracts Annotated with Nested Named Entities

arXiv: https://arxiv.org/abs/2210.11913 · HTML: https://mlsanity.com/paper/2210.11913/

## Key facts

- Cited by 10 papers in the map (data through 14 Oct 2026).
- Builds on 14 of its 37 references that are in the map.
- First posted on arXiv 21 Oct 2022.

## Builds on (most cited first, 14 of 14)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [A Unified MRC Framework for Named Entity Recognition](https://mlsanity.com/paper/1910.11476/) (2019)
- [Adaptation of Deep Bidirectional Multilingual Transformers for Russian Language](https://mlsanity.com/paper/1905.07213/) (2019)
- [An Improved Baseline for Sentence-level Relation Extraction](https://mlsanity.com/paper/2102.01373/) (2021)
- [MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts](https://mlsanity.com/paper/1902.09476/) (2019)
- [BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing](https://mlsanity.com/paper/2206.15076/) (2022)
- [Nested Named Entity Recognition via Second-best Sequence Learning and Decoding](https://mlsanity.com/paper/1909.02250/) (2019)
- [NNE: A Dataset for Nested Named Entity Recognition in English Newswire](https://mlsanity.com/paper/1906.01359/) (2019)
- [DaN+: Danish Nested Named Entities and Lexical Normalization](https://mlsanity.com/paper/2105.11301/) (2021)
- [NEREL: A Russian Dataset with Nested Named Entities, Relations and Events](https://mlsanity.com/paper/2108.13112/) (2021)
- [The Russian Drug Reaction Corpus and Neural Models for Drug Reactions and Effectiveness Detection in User Reviews](https://mlsanity.com/paper/2004.03659/) (2020)
- [RuMedBench: A Russian Medical Language Understanding Benchmark](https://mlsanity.com/paper/2201.06499/) (2022)
- [RuNNE-2022 Shared Task: Recognizing Nested Named Entities](https://mlsanity.com/paper/2205.11159/) (2022)
- [How Do Your Biomedical Named Entity Recognition Models Generalize to Novel Entities?](https://mlsanity.com/paper/2101.00160/) (2021)

## Built on by (most cited first, 10 of 10)

- [Overview of BioASQ 2025: The Thirteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering](https://mlsanity.com/paper/2508.20554/) (2025)
- [Overview of BioASQ 2024: The twelfth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering](https://mlsanity.com/paper/2508.20532/) (2025)
- [Biomedical Nested NER with Large Language Model and UMLS Heuristics](https://mlsanity.com/paper/2407.05480/) (2024)
- [CLARITY: Clinical Assistant for Routing, Inference, and Triage](https://mlsanity.com/paper/2510.02463/) (2025)
- [Automatic Aspect Extraction from Scientific Texts](https://mlsanity.com/paper/2310.04074/) (2023)
- [Research on the Proximity Relationships of Psychosomatic Disease Knowledge Graph Modules Extracted by Large Language Models](https://mlsanity.com/paper/2412.18419/) (2024)
- [RuCCoD: Towards Automated ICD Coding in Russian](https://mlsanity.com/paper/2502.21263/) (2025)
- [Human-Annotated NER Dataset for the Kyrgyz Language](https://mlsanity.com/paper/2509.19109/) (2025)
- [BIBERT-Pipe on Biomedical Nested Named Entity Linking at BioASQ 2025](https://mlsanity.com/paper/2509.09725/) (2025)
- [Overview of BioASQ 2026: The fourteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering](https://mlsanity.com/paper/2609.39975/) (2026)

## Abstract (arXiv)

This paper describes NEREL-BIO -- an annotation scheme and corpus of PubMed abstracts in Russian and smaller number of abstracts in English. NEREL-BIO extends the general domain dataset NEREL by introducing domain-specific entity types. NEREL-BIO annotation scheme covers both general and biomedical domains making it suitable for domain transfer experiments. NEREL-BIO provides annotation for nested named entities as an extension of the scheme employed for NEREL. Nested named entities may cross entity boundaries to connect to shorter entities nested within longer entities, making them harder to detect. NEREL-BIO contains annotations for 700+ Russian and 100+ English abstracts. All English PubMed annotations have corresponding Russian counterparts. Thus, NEREL-BIO comprises the following specific features: annotation of nested named entities, it can be used as a benchmark for cross-domain (NEREL -> NEREL-BIO) and cross-language (English -> Russian) transfer. We experiment with both transformer-based sequence models and machine reading comprehension (MRC) models and report their results. The dataset is freely available at https://github.com/nerel-ds/NEREL-BIO.