PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge

CH Wei, A Allot, PT Lai, R Leaman, S Tian… - Nucleic Acids …, 2024 - academic.oup.com
Abstract PubTator 3.0 (https://www. ncbi. nlm. nih. gov/research/pubtator3/) is a biomedical
literature resource using state-of-the-art AI techniques to offer semantic and relation …

Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes

RAA Jonker, T Almeida, R Antunes, JR Almeida… - Database, 2024 - academic.oup.com
The identification of medical concepts from clinical narratives has a large interest in the
biomedical scientific community due to its importance in treatment improvements or drug …

EnzChemRED, a rich enzyme chemistry relation extraction dataset

PT Lai, E Coudert, L Aimo, K Axelsen, L Breuza… - Scientific Data, 2024 - nature.com
Expert curation is essential to capture knowledge of enzyme functions from the scientific
literature in FAIR open knowledgebases but cannot keep pace with the rate of new …

Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach

MJ Sarol, G Hong, E Guerra, H Kilicoglu - Database, 2024 - academic.oup.com
Biomedical relation extraction from scientific publications is a key task in biomedical natural
language processing (NLP) and can facilitate the creation of large knowledge bases, enable …

BELHD: improving biomedical entity linking with homonym disambiguation

S Garda, U Leser - Bioinformatics, 2024 - academic.oup.com
Motivation Biomedical entity linking (BEL) is the task of grounding entity mentions to a given
knowledge base (KB). Recently, neural name-based methods, system identifying the most …

Towards discovery: an end-to-end system for uncovering novel biomedical relations

T Almeida, RAA Jonker, R Antunes, JR Almeida… - Database, 2024 - academic.oup.com
Biomedical relation extraction is an ongoing challenge within the natural language
processing community. Its application is important for understanding scientific biomedical …

CoSEF-DBP: Convolution scope expanding fusion network for identifying DNA-binding proteins through bilingual representations

H Zhang, X Yang, P Chen, C Yang, B Chen… - Expert Systems with …, 2025 - Elsevier
Precisely recognizing DNA-binding proteins (DBPs) from sequences is crucial for a profound
comprehension of the mechanisms governing protein-DNA interactions in various cellular …

ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature

L Musella, A Afonso Castro, X Lai… - PLOS Computational …, 2025 - journals.plos.org
The accelerating growth of scientific literature overwhelms our capacity to manually distil
complex phenomena like molecular networks linked to diseases. Moreover, biases in …

[PDF][PDF] Correspondence on “Comparison of literature mining tools for variant classification: through the lens of 50 RYR1 variants” by Wermers et al

CH Wei, L Phan, T Hefferon, M Landrum, HL Rehm… - Genet Med, 2024 - ryr1.org
To the Editor: We read with interest the recent study by Zara Wermers and colleagues1 that
analyzed the utility of different databases and literature mining tools for the classification of …

Assessing Artificial Intelligence (AI) Implementation for Assisting Gene Linking (at the National Library of Medicine)

R Islamaj, CH Wei, PT Lai, M Huston, C Coss… - JAMIA …, 2025 - academic.oup.com
Abstract Objectives The National Library of Medicine (NLM) currently indexes close to a
million articles each year pertaining to more than 5300 medicine and life sciences journals …