mlsanityData to 7 Oct 2026

MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts

arXiv 1902.09476 ↗First posted 25 Feb 2019cs.CL cs.LGcited by 79

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Abstract (arXiv)

This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts and over 350,000 linked mentions), as well as the size of the concept ontology (over 3 million concepts from UMLS 2017) and its broad coverage of biomedical disciplines. In addition to the full corpus, a sub-corpus of MedMentions is also presented, comprising annotations for a subset of UMLS 2017 targeted towards document retrieval. To encourage research in Biomedical Named Entity Recognition and Linking, data splits for training and testing are included in the release, and a baseline model and its metrics for entity linking are also described.

Key facts. Cited by 79 papers in the map (data through 7 Oct 2026). First posted on arXiv 25 Feb 2019.

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Citing papers per year: 2021: 14; 2022: 10; 2023: 17; 2024: 17; 2025: 7; 2026: 14.

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  1. 2022BioBART: Pretraining and Evaluation of A Biomedical Generative Language Modelcited by 83
  2. 2022Generating Scientific Claims for Zero-Shot Scientific Fact Checkingcited by 59
  3. 2024SciRIFF: A Resource to Enhance Language Model Instruction-Following over Scientific Literaturecited by 37
  4. 2022BigBIO: A Framework for Data-Centric Biomedical Natural Language Processingcited by 36
  5. 2022Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuningcited by 34
  6. 2021AMMU : A Survey of Transformer-based Biomedical Pretrained Language Modelscited by 32
  7. 2021Knowledge-Rich Self-Supervision for Biomedical Entity Linkingcited by 31
  8. 2024Data-Centric Foundation Models in Computational Healthcare: A Surveycited by 27
  9. 2021Entity Linking and Discovery via Arborescence-based Supervised Clusteringcited by 22
  10. 2022BioLORD: Learning Ontological Representations from Definitions (for Biomedical Concepts and their Textual Descriptions)cited by 20
  11. 2023ECG-Image-Kit: A Synthetic Image Generation Toolbox to Facilitate Deep Learning-Based Electrocardiogram Digitizationcited by 20
  12. 2024ReflecTool: Towards Reflection-Aware Tool-Augmented Clinical Agentscited by 20
38 more
  1. 2024Unveiling LLM Evaluation Focused on Metrics: Challenges and Solutionscited by 17
  2. 2021Fast and Effective Biomedical Entity Linking Using a Dual Encodercited by 16
  3. 2025Multimodal Large Language Models for Medicine: A Comprehensive Surveycited by 16
  4. 2021Cross-Domain Data Integration for Named Entity Disambiguation in Biomedical Textcited by 15
  5. 2021BERT might be Overkill: A Tiny but Effective Biomedical Entity Linker based on Residual Convolutional Neural Networkscited by 14
  6. 2023TempEL: Linking Dynamically Evolving and Newly Emerging Entitiescited by 14
  7. 2021A Search Engine for Discovery of Scientific Challenges and Directionscited by 12
  8. 2023SpEL: Structured Prediction for Entity Linkingcited by 11
  9. 2022NEREL-BIO: A Dataset of Biomedical Abstracts Annotated with Nested Named Entitiescited by 10
  10. 2022Computer Science Named Entity Recognition in the Open Research Knowledge Graphcited by 9
  11. 2024On-the-fly Definition Augmentation of LLMs for Biomedical NERcited by 9
  12. 2023Biomedical Language Models are Robust to Sub-optimal Tokenizationcited by 8
  13. 2024HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization toolscited by 8
  14. 2024KcMF: A Knowledge-compliant Framework for Schema and Entity Matching with Fine-tuning-free LLMscited by 8
  15. 2021How Do Your Biomedical Named Entity Recognition Models Generalize to Novel Entities?cited by 7
  16. 2023Reveal the Unknown: Out-of-Knowledge-Base Mention Discovery with Entity Linkingcited by 7
  17. 2023Ontology Enrichment from Texts: A Biomedical Dataset for Concept Discovery and Placementcited by 7
  18. 2023BELB: a Biomedical Entity Linking Benchmarkcited by 7
  19. 2024Generalizable and Scalable Multistage Biomedical Concept Normalization Leveraging Large Language Modelscited by 7
  20. 2024MedINST: Meta Dataset of Biomedical Instructionscited by 7
  21. 2021Improved Latent Tree Induction with Distant Supervision via Span Constraintscited by 6
  22. 2024Learning from Negative Samples in Biomedical Generative Entity Linkingcited by 6
  23. 2024MEG: Medical Knowledge-Augmented Large Language Models for Question Answeringcited by 6
  24. 2021Biomedical Entity Linking with Contrastive Context Matchingcited by 5
  25. 2023GLADIS: A General and Large Acronym Disambiguation Benchmarkcited by 5
  26. 2021Zero-shot Medical Entity Retrieval without Annotation: Learning From Rich Knowledge Graph Semanticscited by 4
  27. 2021Biomedical Interpretable Entity Representationscited by 4
  28. 2022Longtonotes: OntoNotes with Longer Coreference Chainscited by 4
  29. 2024BELHD: Improving Biomedical Entity Linking with Homonoym Disambiguationcited by 4
  30. 2024DynamicER: Resolving Emerging Mentions to Dynamic Entities for RAGcited by 4
  31. 2021Low Resource Recognition and Linking of Biomedical Concepts from a Large Ontologycited by 3
  32. 2023Span-based Named Entity Recognition by Generating and Compressing Informationcited by 3
  33. 2023Evaluating end-to-end entity linking on domain-specific knowledge bases: Learning about ancient technologies from museum collectionscited by 3
  34. 2023xMEN: A Modular Toolkit for Cross-Lingual Medical Entity Normalizationcited by 3
  35. 2024Variable Extraction for Model Recovery in Scientific Literaturecited by 3
  36. 2022MedDistant19: Towards an Accurate Benchmark for Broad-Coverage Biomedical Relation Extractioncited by 2
  37. 2023Proxy-based Zero-Shot Entity Linking by Effective Candidate Retrievalcited by 2
  38. 2023Exploring Partial Knowledge Base Inference in Biomedical Entity Linkingcited by 2

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