Overview of CHIP 2026 Shared Task 1: Patient-Specific Phenotype Concept Recognition in Full-Text Biomedical Literature

Xuanlyu Zhu, Feng Tian, Yang Zhong, Pengqi Zheng, Xiwen Bi +4

Automatic phenotype information extraction plays an important role in rare disease diagnosis, genotype-phenotype analysis, and precision medicine. However, accurately identifying phenotype concepts and determining their associations with specific patients remain challenging, particularly in full-text biomedical articles involving multiple patients and complex clinical descriptions. This paper presents an overview of CHIP 2026 Shared Task 1, which aims to promote the development of methods for patient-specific phenotype concept recognition from full-text biomedical literature. The task consists of two subtasks: full-text phenotype concept recognition and patient-specific phenotype association. For this evaluation, we used 200 annotated full-text biomedical articles from the PatientPheX dataset, containing 506 patients, 15,193 phenotype mentions, and 5,656 patient-phenotype associations. A total of 455 teams registered for the competition, with 189 and 103 valid submissions received on the Phase A and Phase B leaderboards, respectively. The best-performing system achieved an overall score of 0.7389 on the final test set, outperforming the baseline by 8.37 percentage points. The…