1.Sanren Runchang Formula Regulates Brain-gut Axis to Treat IBS-C: A Randomized Controlled Trial
Teng LI ; Xinrong FAN ; He YAN ; Zhuozhi GONG ; Mengxi YAO ; Na YANG ; Yuhan WANG ; Huikai HU ; Wei WEI ; Tao LIU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(2):154-161
ObjectiveTo observe the clinical efficacy of Sanren Runchang formula in treating constipation-predominant irritable bowel syndrome (IBS-C) by regulating the brain-gut axis and the effects of the formula on serum levels of 5-hydroxytryptamine (5-HT), vasoactive intestinal peptide (VIP), and substance P (SP). MethodsA randomized controlled design was adopted, and 72 IBS-C patients meeting Rome Ⅳ criteria were randomized into observation and control groups (36 cases).The observation group received Sanren Runchang formula granules twice daily, and the control group received lactulose oral solution daily for 4 weeks. IBS Symptom Severity Scale (IBS-SSS), IBS Quality of Life Scale (IBS-QOL), and Bristol Stool Form Scale (BSFS) were used to assess clinical symptoms, and bowel movement frequency was recorded. The Self-Rating Anxiety Scale (SAS) and Self-Rating Depression Scale (SDS) were employed to evaluate psychological status. ELISA was employed to measure the serum levels of 5-HT, VIP, and SP. ResultsThe total response rate in the observation group was 91.67% (33/36), which was higher than that (77.78%, 28/36) in the control group (χ2=4.50, P<0.05). After treatment, both groups showed increased defecation frequency and BSFS scores, decreased IBS-SSS total score, abdominal pain and bloating scores, IBS-QOL health anxiety, anxiety, food avoidance, and behavioral disorders scores, SAS and SDS scores, serum 5-HT and VIP levels, and increased SP levels (P<0.05, P<0.01). Moreover, the observation group showed more significant changes in the indicators above than the control group (P<0.05, P<0.01). The SP level showed no significant difference between the two groups. During the 4-week follow-up, the recurrence rate was 5.88% in the observation group and 31.25% in the control group. No adverse events occurred in observation group, and 2 cases of mild diarrhea occurred in the control group. ConclusionSanren Runchang formula demonstrated definitive efficacy in alleviating gastrointestinal symptoms and improving the psychological status and quality of life in IBS-C patients, with a low recurrence rate. The formula can regulate serum levels of neurotransmitters such as 5-HT and VIP, suggesting its potential regulatory effect on the brain-gut axis through modulating neurotransmitters and neuropeptides. However, its complete mechanism of action requires further investigation through detection of additional brain-gut axis-related biomarkers.
2.Characterization and Application of Moisture Absorption Kinetics of Traditional Chinese Medicines Based on Double Exponential Model:A Review
Yanting YU ; Lei XIONG ; Yan HE ; Wei LIU ; Jing YANG ; Yao ZHANG ; Jiali CHEN ; Xiaojian LUO ; Xiaoyong RAO
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(5):340-346
Hygroscopicity research has long been a key focus and hot topic in Chinese materia medica(CMM). Elucidating hygroscopic mechanisms plays a vital role in formulation design, process optimization, and storage condition selection. Hygroscopic models serve as essential tools for characterizing CMM hygroscopic mechanisms, with various types available. The double exponential model is a kinetic mathematical model constructed based on the law of conservation of energy and Fick's first law of diffusion, tailored to the physical properties of CMM extracts. In recent years, this model has been extensively applied to simulate the dynamic moisture absorption behavior of CMM extracts and solid dosage forms under varying humidity conditions. It has revealed the correlation between moisture absorption kinetic parameters and material properties, offering a new perspective for characterizing the moisture uptake behavior of CMM. This paper systematically reviews the application progress of this model in the field of CMM, analyzes its advantages, disadvantages, and challenges in this domain, and explores its potential application trends in other fields. It aims to provide references for elucidating the moisture absorption mechanisms of CMM and researching moisture-proofing technologies, while also offering insights for its broader application in food and polymer materials.
3.Analysis of Blood-absorbed Components and Their Metabolic Differences of Xiebaisan in Normal and Chronic Bronchitis Mice Based on UPLC-Q-Exactive Orbitrap MS
Peng PENG ; Jiaxin LI ; Xinyue YANG ; Fangle LIU ; Chenchen ZHU ; Chaozhan LIN ; Yufeng YAO
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(1):219-227
ObjectiveThis study aims to systematically analyze the blood-absorbed components and metabolic profiles of Xiebaisan(XBS) in normal and chronic bronchitis (CB) mice using ultra performance liquid chromatography-quadrupole-electrostatic field orbitrap high resolution mass spectrometry(UPLC-Q-Exactive Orbitrap MS), while comparing differences between the two states. MethodsThirty female BABL/c mice were randomly divided into the normal group, the normal drug administration group, the CB group, the CB drug administration group and the dexamethasone group, with 6 mice in each group. The CB mouse model was established by inducing with ovalbumin (OVA). The mice in the normal drug administration group and the CB drug administration group started to be gavaged with XBS(13.2 g·kg-1) from the 21st day, and the dexamethasone group mice were simultaneously gavaged with dexamethasone (0.5 mg·kg-1) until the end of the 35th day of the experiment. Subsequently, serum samples were collected and evaluated for their efficacy, based on the pharmacological evaluation indicators, to determine the efficacy of XBS in treating CB. Then the UPLC-Q-Exactive Orbitrap MS was employed to identify and analyze the chemical constituents, blood-absorbed components, and metabolites of XBS. Chemometric analysis was conducted to reveal metabolic profile differences under "dual states". Concurrently, Real-time PCR technology was utilized to detect the expression levels of key liver metabolic enzymes CYP2E1, CYP3A1, UGT1A1, and UGT1A6. ResultsA total of 28 prototype components and 158 metabolites (including 48 phase Ⅰ metabolites and 110 phase Ⅱ metabolites) of XBS were unambiguously identified in the serum of normal mice. Additionally, a comprehensive characterization was performed on a total of 32 prototype components and 178 metabolites (including 50 phase Ⅰ metabolites and 128 phase Ⅱ metabolites) of XBS in the serum of CB mice. Among them, 27 prototype components were detected in both states, including 12 flavonoids, 2 alkaloids, 3 triterpenes, 4 organic acids, 3 amides, 1 stilbene and 2 other compounds. The chemometrics analysis revealed no significant difference in the prototype components and metabolites of XBS between normal and CB mice; however, there was a significant increase in the in-vivo exposure of XBS in CB mice. Compared to normal mice, the levels of phase Ⅰ metabolites such as oxidation, reduction and methylation of blood components of XBS as well as phase Ⅱ metabolites of glucuronidation showed significant changes in CB mice. Real-time PCR further confirmed that these alterations were attributed to the upregulation of CYP2E1 (P<0.05), CYP3A1 (P>0.05), UGT1A1 (P<0.01) and UGT1A6 (P<0.01) enzymes expression in the liver of CB mice. ConclusionThis study elucidated the disparities in the levels of the blood-absorbed components and metabolic profiles of XBS in normal and CB mice, especially in oxidation, reduction, methylation in phase Ⅰ metabolism and glucoaldehyde acidification in phase Ⅱ metabolism. And there are related to the differences in the expression levels of phase Ⅰ and phase Ⅱ metabolic enzymes CYP2E1, CYP3A1, UGT1A1 and UGT1A6 in the liver.
4.Investigating Effect of Xianglian Huazhuo Prescription on Cell Cycle and Proliferation in Rats with Chronic Atrophic Gastritis Through TGF-β1/Smads Signaling Pathway
Yican WANG ; Jie WANG ; Yirui CHENG ; Xiaojing LI ; Yibin MA ; Qiuhua LIU ; Ziwei LIU ; Yuxi GUO ; Pengli DU ; Yanru CAI ; Yao DU ; Zheng ZHI ; Bolin LI ; Qian YANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):128-136
ObjectiveTo explore the potential mechanism of Xianglian Huazhuo prescription (XLHZ) in treating chronic atrophic gastritis (CAG) by regulating cell cycle and inhibiting proliferation, using bioinformatics technology and animal experiments. MethodsDifferential expressed genes (DEGs) related to CAG were screened using GEO database and GEO2R tool. Weighted gene co-expression network analysis (WGCNA) was employed to search for hub genes of CAG. These hub genes were intersected with cell cycle proliferation based on GeneCards database. Eenrichment analysis of the intersecting genes was performed to obtain signaling pathways and biological processes related to CAG. Protein protein interaction (PPI) analysis of genes was conducted using the Protein Interaction Platform (STRING) database to search the super hub gene (hub 2.0), and animal experiments were conducted for further validation. Fourteen of 70 male Wistar rats were randomly selected as the normal group, and the remaining 56 rats were prepared by the combined modeling method of "starvation disorder+N-methyl-N-nitro-N-nitrosoguanidine (MNNG) + sodium salicylate". The successfully modeled rats were randomly divided into the model group, XLHZ-H, XLHZ-M, and XLHZ-L groups (36, 18, 9 g·kg-1, respectively), and Morodan group (1.4 g·kg-1). Each group was given corresponding intervention for 60 days. Hematoxylin-eosin (HE) staining was used to observe the histopathological changes of gastric mucosa in rats. The ultrastructure of gastric mucosal tissue cells was observed by transmission electron microscopy. The relative expression levels of TGF-β1, Smad2 and Smad3 proteins, S/G2/M phase marker geminin and proliferation marker MCM2 were detected by Western blot in gastric mucosal tissue, and Spearman correlation analysis was performed. ResultsA total of 15 hub 2.0 genes were identified, including TGF-β1, suggesting the involvement of the TGF-β1 signaling pathway in the CAG pathogenesis. Compared with the normal group, the expressions of TGF-β1, Smad2, geminin and MCM2 proteins in the gastric mucosa tissue of the model group were increased (P<0.05), and the expression of Smad3 protein was decreased (P<0.05). Compared with the model group, the expressions of TGF-β1 and geminin in the gastric mucosa were decreased in the drug groups (P<0.05). The XLHZ-M group, XLHZ-H group and Morodan group had significantly decreased protein expression of Smad2 and MCM2 (P<0.05). The protein expression of Smad3 was significantly increased in XLHZ-M, XLHZ-H, and Morodan groups (P<0.05). Spearman correlation analysis showed that Smad3 was negatively correlated with other indicators, and positively correlated with other indicators (P<0.01). ConclusionXLHZ may inhibit TGF-β1/Smads signaling pathway, regulate cell cycle, and inhibit proliferation in the treatment of CAG.
5.Investigating Effect of Xianglian Huazhuo Prescription on Cell Cycle and Proliferation in Rats with Chronic Atrophic Gastritis Through TGF-β1/Smads Signaling Pathway
Yican WANG ; Jie WANG ; Yirui CHENG ; Xiaojing LI ; Yibin MA ; Qiuhua LIU ; Ziwei LIU ; Yuxi GUO ; Pengli DU ; Yanru CAI ; Yao DU ; Zheng ZHI ; Bolin LI ; Qian YANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):128-136
ObjectiveTo explore the potential mechanism of Xianglian Huazhuo prescription (XLHZ) in treating chronic atrophic gastritis (CAG) by regulating cell cycle and inhibiting proliferation, using bioinformatics technology and animal experiments. MethodsDifferential expressed genes (DEGs) related to CAG were screened using GEO database and GEO2R tool. Weighted gene co-expression network analysis (WGCNA) was employed to search for hub genes of CAG. These hub genes were intersected with cell cycle proliferation based on GeneCards database. Eenrichment analysis of the intersecting genes was performed to obtain signaling pathways and biological processes related to CAG. Protein protein interaction (PPI) analysis of genes was conducted using the Protein Interaction Platform (STRING) database to search the super hub gene (hub 2.0), and animal experiments were conducted for further validation. Fourteen of 70 male Wistar rats were randomly selected as the normal group, and the remaining 56 rats were prepared by the combined modeling method of "starvation disorder+N-methyl-N-nitro-N-nitrosoguanidine (MNNG) + sodium salicylate". The successfully modeled rats were randomly divided into the model group, XLHZ-H, XLHZ-M, and XLHZ-L groups (36, 18, 9 g·kg-1, respectively), and Morodan group (1.4 g·kg-1). Each group was given corresponding intervention for 60 days. Hematoxylin-eosin (HE) staining was used to observe the histopathological changes of gastric mucosa in rats. The ultrastructure of gastric mucosal tissue cells was observed by transmission electron microscopy. The relative expression levels of TGF-β1, Smad2 and Smad3 proteins, S/G2/M phase marker geminin and proliferation marker MCM2 were detected by Western blot in gastric mucosal tissue, and Spearman correlation analysis was performed. ResultsA total of 15 hub 2.0 genes were identified, including TGF-β1, suggesting the involvement of the TGF-β1 signaling pathway in the CAG pathogenesis. Compared with the normal group, the expressions of TGF-β1, Smad2, geminin and MCM2 proteins in the gastric mucosa tissue of the model group were increased (P<0.05), and the expression of Smad3 protein was decreased (P<0.05). Compared with the model group, the expressions of TGF-β1 and geminin in the gastric mucosa were decreased in the drug groups (P<0.05). The XLHZ-M group, XLHZ-H group and Morodan group had significantly decreased protein expression of Smad2 and MCM2 (P<0.05). The protein expression of Smad3 was significantly increased in XLHZ-M, XLHZ-H, and Morodan groups (P<0.05). Spearman correlation analysis showed that Smad3 was negatively correlated with other indicators, and positively correlated with other indicators (P<0.01). ConclusionXLHZ may inhibit TGF-β1/Smads signaling pathway, regulate cell cycle, and inhibit proliferation in the treatment of CAG.
6.Analysis of undernutrition and associated factors among left behind and nonleftbehind primary and secondary school students in the Nutrition Improvement Program areas in central and western China
Chinese Journal of School Health 2026;47(3):327-331
Objective:
To investigate the prevalence of undernutrition and its associated factors among left behind and non left behind primary and secondary school students in the Nutrition Improvement Program for Rural Compulsory Education Students (NIPRCES) areas of central and western China, so as to provide evidence for improving the nutritional status of children and adolescents.
Methods:
A survey was conducted among 123 782 students selected by random cluster sampling method in grades 3-9 from NIPRCES in central (Hebei, Shanxi, Heilongjiang, Jilin, Anhui, Jiangxi, Henan, Hunan, Hubei, and Hainan) and western (Gansu, Guangxi, Inner Mongolia, Ningxia, Tibet, Shaanxi, Guizhou, Sichuan, Xinjiang, the Xinjiang Production and Construction Corps, Yunnan, Qinghai, and Chongqing) China in 2023. Anthropometric measurements and questionnaires were used to assess nutritional and dietary status. The prevalence of undernutrition was compared between left behind and non left behind students by Chi square test, and associated factors were analyzed by three level Logistic mixed effects model.
Results:
The prevalence of undernutrition was 8.5% (4 326) in left behind students and 8.1% (5 905) in non left behind students. Three level Logistic mixed effect model analysis showed that whether left behind or non left behind, the undernutrition rates of primary and secondary students in western regions were higher than those of students in central regions [ OR (95% CI )=1.72(1.57-1.87),2.25(2.07- 2.43 )]; the undernutrition risk was lower for those whose fathers had a cultural level of high school or above [ OR (95% CI )=0.69(0.62-0.77),0.90(0.82-0.98)] or junior high school [ OR (95% CI )=0.72(0.66-0.79),0.92(0.85-0.99)] compared to those with primary school or below; picky eating or selective eating increased the risk of undernutrition [ OR (95% CI )=2.36(2.07-2.68),2.28(2.04-2.55)], and primary and secondary school students without nutritional content in health education classes had higher rates of undernutrition [ OR (95% CI )=1.12(1.03-1.23),1.09(1.01-1.17)](all P <0.05).
Conclusion
The prevalence of undernutrition is slightly higher in left behind primary and secondary students than in non left behind primary and secondary students in central and western NIPRCES areas, with variations across different characteristics.
7.Impact of DRG payment on length of stay and medical costs in COPD patients from Kashgar region
Jiale YANG ; Ningning WANG ; Aierken AIZEZIJIANG ; Lingkai LIAN ; Xinyi LYU ; Pengcheng LIU ; Wenbing YAO
China Pharmacy 2026;37(8):991-997
OBJECTIVE To analyze the impact of the diagnosis-related groups (DRG) payment reform on the length of stay and medical costs in patients with chronic obstructive pulmonary disease (COPD) in Kashgar region, aiming to provide localized empirical evidence for the optimization of regional medical insurance payment methods. METHODS Based on the inpatient settlement database of the Xinjiang Uygur Autonomous Region Healthcare Security Administration, settlement data of COPD inpatients from 17 medical institutions in Kashgar region between January 1, 2022, and December 31, 2024, were extracted. The overall changes in patients’ length of stay and costs were compared before and after the reform. Subsequently, interrupted time series analysis (ITSA) was employed to explore the impact of the DRG payment reform on these variables. RESULTS Following the reform, both the average length of stay and various cost decreased significantly compared to the pre-reform period ( P <0.001). At the overall sample level, the average length of stay, average total cost, average drug cost, average medical service cost, and average examination cost per admission all demonstrated significant long-term downward trends after the reform ( P <0.05). However, the decrease in average out-of-pocket costs and the increase in average consumable costs per admission were not statistically significant ( P >0.05). In tertiary medical institutions, the average length of stay and all categories of costs (except average consumable costs per admission) exhibited significant long-term upward trends after the reform ( P <0.05); conversely, in secondary and lower-level medical institutions, the average length of stay, average total cost, average drug cost, average medical service cost, and average examination cost per admission showed significant long-term downward trends ( P <0.05). CONCLUSIONS The DRG payment reform has achieved an overall effect of reducing the length of stay and controlling costs in COPD patients from Kashgar region. However, the effects vary across different levels of medical institutions: secondary and lower-level institutions show a long-term downward trend in length of stay and costs, whereas tertiary institutions exhibit a long-term upward trend. Furthermore, patients’ out-of-pocket financial burden does not show significant improvement.
8.Evidence-based evaluation and hierarchical management of off-label use of 5-aminolevulinic acid in photodynamic therapy
Jing MA ; Tingting LIU ; Xiaoshuang GOU ; Xue YANG ; Chen LI ; Fang LIU ; Yao LIU
China Pharmacy 2026;37(8):1056-1061
OBJECTIVE To provide reference for medical institutions to establish the record management mode and review rules of off-label use of 5-aminolevulinic acid (ALA) in photodynamic therapy based on the level of evidence. METHODS All ALA-containing outpatient prescriptions in the rational drug use system in our hospital from January 1, 2024 to December 31, 2025 were retrospectively collected. Based on the drug instructions, the current status of off-label use of ALA in photodynamic therapy was identified . The relevant studies in Micromedex, PubMed, CNKI, Wanfang Data and other databases were systematically searched as the relevant evidence-based evidence of ALA off-label use. According to the Off-label Drug Use Filing Standard of the hospital,the evidence-based evaluation method was used to evaluate the evidence-based evidence of ALA off-label use and carry out hierarchical management. RESULTS A total of 1 803 effective prescriptions were included, of which 676 (37.49%) were off-label use, distributed in the dermatology department (564 prescriptions,83.43%) and the plastic surgery department (112 prescriptions,16.57%). All 676 prescriptions were off-indications medication, involving ten types of skin diseases, primarily including moderate to severe acne (39.94%), skin warts (25.44%), Bowen’s disease (11.98%), and others. According to evidence-based evidence,off-label uses such as moderate to severe acne, actinic keratosis, and Bowen’s disease were managed according to the evidence categoryⅠ orⅡ.The uses of extramammary Paget’s disease and rosacea were managed according to the evidence category Ⅲ.The uses of lichen sclerosus and keloids were managed according to the evidence category Ⅳ.The results of evidence-based evaluation showed that 92.01% of off-label use in our hospital had high-level evidence-based support ( evidence category was gradeⅠ-Ⅱ). CONCLUSIONS Off-label uses supported by high-level evidence, such as moderate to severe acne, skin warts, and Bowen’s disease, can be managed under filing category Ⅰ or Ⅱ. For the use of lichen sclerosus and keloids, evidence-based evidence is insufficient and should be strictly restricted.The vast majority of ALA off-label use in our hospital has sufficient evidence-based basis.
9.Influence of Antigen Type on the Establishment of an Induced Sjögren Syndrome Mouse Model
Wenshuang RONG ; Yuanfei NIU ; Meiting LIU ; Mengyuan YANG ; Shuang CUI ; Lina MA ; Yao FU ; Lianmei WANG ; Junling CAO
Laboratory Animal and Comparative Medicine 2026;46(2):178-190
ObjectiveThis study aims to compare the modeling effects of submaxillary gland antigen and salivary gland antigen in the establishment of Sjögren syndrome (SS) mouse models, and to characterize the phenotypic and immunological features of these models in comparison with spontaneous SS-prone non-obese diabetic (NOD)/LtJ mice. MethodsAdult C57BL/6J mice (equal numbers of males and females) were immunized with submaxillary gland antigen or salivary gland antigen, respectively, combined with Freund's adjuvant to induce SS models. Mice immunized with phosphate-buffered saline (PBS) combined with Freund's adjuvant served as the control group. Immunization was induced via multiple subcutaneous injections in the back with antigen combined with Freund's complete adjuvant (FCA) on Days 1 and 7. A booster immunization was administered via multiple subcutaneous injections in the back with antigen combined with Freund's incomplete adjuvant (FIA) on Day 14. Female NOD/LtJ mice were used as the spontaneous SS model group, with ICR mice as the corresponding control strain for comparative analysis. Body weight, water intake, and salivary flow rate of mice were dynamically monitored for 4 weeks. At the end of the experiment, tissue and serum samples were collected, the weights of submaxillary glands, thymus, and spleen were measured, and organ indices (organ-to-body weight ratios) were calculated. Pathological morphological analysis of the submaxillary gland and spleen was performed with hematoxylin and eosin (HE) staining. Serum interleukin-17 (IL-17) level was detected using enzyme-linked immunosorbent assay (ELISA). Real-time quantitative polymerase chain reaction was used to detect the mRNA expression levels of SS type A (SSA) and SS type B (SSB) in submaxillary gland tissues. ResultsFemale mice in the submaxillary gland antigen group exhibited significantly increased water intake (P<0.05) and reduced salivary flow rate (P<0.05) compared with the female control group. No statistically significant differences were observed in the submaxillary gland index, thymus index and spleen index (P>0.05). Focal lymphocytic infiltration was observed in the submaxillary glands, and the splenic marginal zone was enlarged. Serum IL-17 levels were significantly increased (P<0.05). There was no significant difference in submaxillary gland SSA/SSB expression levels (P>0.05). Compared with the female control group, female mice in the salivary gland antigen group showed no statistically significant differences in water intake, salivary flow rate, submaxillary gland index, and spleen index (P>0.05), whereas the thymus index was significantly reduced (P<0.01). Mild inflammatory cell infiltration and glandular atrophy were observed in the submaxillary glands, and the splenic white pulp and marginal zone were slightly enlarged. Serum IL-17 levels and submaxillary gland SSB mRNA expression levels were significantly increased (P<0.01), whereas no significant change was observed in submaxillary gland SSA expression levels (P>0.05). Compared with the male control group, mild submaxillary gland atrophy was observed in male mice in the submaxillary gland antigen group, whereas no obvious changes were found in other modeling-related indicators (P>0.05). Compared with the ICR control group, NOD/LtJ model mice exhibited elevated water intake (P<0.05), significantly reduced salivary flow rate (P<0.01), no significant differences in the submaxillary gland index or spleen index (P>0.05), but a significantly increased thymus index (P<0.05). Marked focal infiltration was observed in the submaxillary glands, the splenic marginal zone was obviously enlarged, and serum IL-17 concentrations as well as submaxillary gland SSA/SSB expression levels were significantly increased (P<0.05). ConclusionSubmaxillary gland antigen and salivary gland antigen can induce SS-related features in female C57BL/6J mice. The SS-related phenotype is more pronounced in the submaxillary gland antigen group than in the salivary gland antigen group, but weaker than that in spontaneously SS-prone female NOD/LtJ mice. Immunization of male C57BL/6J mice with submaxillary or salivary gland antigens fails to induce an obvious SS phenotype.
10.Development and validation of PhenoRAG: A visualization tool for automated human phenotype ontology term annotation based on large language models and retrieval-augmented generation technology.
Wei ZHONG ; Yousheng YAN ; Kai YANG ; Yan LIU ; Xinyu FU ; Zhengyang YAO ; Chenghong YIN
Chinese Journal of Medical Genetics 2026;43(1):36-43
OBJECTIVE:
To develop a user-friendly visualization application for the automatic annotation of Human Phenotype Ontology (HPO) terms based on large language models and retrieval-augmented generation (RAG) technology, and to validate its performance in an authoritative case dataset.
METHODS:
By integrating the domestic open-source large language model DeepSeek-V3 with RAG technology, an interactive web application was deployed on the Streamlit cloud platform. Using only the latest official HPO dataset as the data source, the lightweight sentence-embedding model BAAI/bge-small-en-v1.5 was employed to construct a FAISS vector index. During the online phase, a four-step closed-loop process is automatically completed: multilingual translation, phenotype phrase extraction, RAG candidate retrieval, term mapping, and official database validation. 121 English case reports publicly released by BMJ Case Reports and Oxford Medical Case Reports (with a gold-standard HPO set of 1 794 terms) were selected for application validation. Precision, recall, and F1 score were calculated and compared horizontally with traditional dictionary tools, standalone large language models, and the similar application "RAG-HPO". Finally, replace the model with the more advanced ChatGPT-5 and evaluate its performance on the newly extracted dataset.
RESULTS:
An HPO term automatic annotation visualization application named PhenoRAG, based on large language models and RAG technology, was successfully developed. Users can access it directly via a web link. Across the 112 cases, a total of 2 150 HPO terms were generated; 2,064 (96.0%) were fully validated by the official database, with a hallucination rate of 1.3% and an HPO ID-name mismatch rate of 2.7%. After deduplication, 1,906 terms remained for testing. The overall precision was 63.65%, recall was 67.34%, and F1 was 65.44%, significantly outperforming traditional annotation tools (F1: 0.45-0.49, P < 0.001). Although PhenoRAG's F1 was lower than that of RAG-HPO (F1 = 0.78, P < 0.001), which relies on a manually constructed synonym database of 54 000 entries plus the HPO dataset, it requires no additional dictionary maintenance and can be used without any background in computer programming. Moreover, after switching to the GPT-5 model, PhenoRAG exhibited no hallucination rate on the new dataset, and its F1 score significantly increased (P = 0.038).
CONCLUSION
Without constructing a synonym database, the PhenoRAG achieved high-accuracy automatic mapping from clinical text to standard HPO terms. It features a low usage threshold, free access, and a Chinese-language interface, and can directly serve rare disease diagnosis, genetic counseling, and research scenarios in China and worldwide, warranting further clinical promotion and multicenter validation.
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Phenotype
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Biological Ontologies
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Large Language Models


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