1
|
Dashti M, Ghasemi S, Ghadimi N, Hefzi D, Karimian A, Zare N, Fahimipour A, Khurshid Z, Chafjiri MM, Ghaedsharaf S. Performance of ChatGPT 3.5 and 4 on U.S. dental examinations: the INBDE, ADAT, and DAT. Imaging Sci Dent 2024; 54:271-275. [PMID: 39371301 PMCID: PMC11450412 DOI: 10.5624/isd.20240037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/21/2024] [Accepted: 04/27/2024] [Indexed: 10/08/2024] Open
Abstract
Purpose Recent advancements in artificial intelligence (AI), particularly tools such as ChatGPT developed by OpenAI, a U.S.-based AI research organization, have transformed the healthcare and education sectors. This study investigated the effectiveness of ChatGPT in answering dentistry exam questions, demonstrating its potential to enhance professional practice and patient care. Materials and Methods This study assessed the performance of ChatGPT 3.5 and 4 on U.S. dental exams - specifically, the Integrated National Board Dental Examination (INBDE), Dental Admission Test (DAT), and Advanced Dental Admission Test (ADAT) - excluding image-based questions. Using customized prompts, ChatGPT's answers were evaluated against official answer sheets. Results ChatGPT 3.5 and 4 were tested with 253 questions from the INBDE, ADAT, and DAT exams. For the INBDE, both versions achieved 80% accuracy in knowledge-based questions and 66-69% in case history questions. In ADAT, they scored 66-83% in knowledge-based and 76% in case history questions. ChatGPT 4 excelled on the DAT, with 94% accuracy in knowledge-based questions, 57% in mathematical analysis items, and 100% in comprehension questions, surpassing ChatGPT 3.5's rates of 83%, 31%, and 82%, respectively. The difference was significant for knowledge-based questions (P=0.009). Both versions showed similar patterns in incorrect responses. Conclusion Both ChatGPT 3.5 and 4 effectively handled knowledge-based, case history, and comprehension questions, with ChatGPT 4 being more reliable and surpassing the performance of 3.5. ChatGPT 4's perfect score in comprehension questions underscores its trainability in specific subjects. However, both versions exhibited weaker performance in mathematical analysis, suggesting this as an area for improvement.
Collapse
Affiliation(s)
- Mahmood Dashti
- Dentofacial Deformities Research Center, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shohreh Ghasemi
- Department of Trauma and Craniofacial Reconstruction, Queen Mary College, London, England
| | - Niloofar Ghadimi
- Department of Oral and Maxillofacial Radiology, Dental School, Islamic Azad University of Medical Sciences, Tehran, Iran
| | - Delband Hefzi
- School of Dentistry, Tehran University of Medical Science, Tehran, Iran
| | - Azizeh Karimian
- Department of Biostatistics, Dental Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Niusha Zare
- Department of Operative Dentistry, University of Southern California, CA, USA
| | - Amir Fahimipour
- Discipline of Oral Surgery, Medicine and Diagnostics, School of Dentistry, Faculty of Medicine and Health, Westmead Centre for Oral Health, The University of Sydney, Sydney, Australia
| | - Zohaib Khurshid
- Department of Prosthodontics and Dental Implantology, King Faisal University, Al Ahsa, Kingdom of Saudi Arabia
| | - Maryam Mohammadalizadeh Chafjiri
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sahar Ghaedsharaf
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
2
|
Wang Y, Liang L, Li R, Wang Y, Hao C. Comparison of the Performance of ChatGPT, Claude and Bard in Support of Myopia Prevention and Control. J Multidiscip Healthc 2024; 17:3917-3929. [PMID: 39155977 PMCID: PMC11330241 DOI: 10.2147/jmdh.s473680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 07/25/2024] [Indexed: 08/20/2024] Open
Abstract
Purpose Chatbots, which are based on large language models, are increasingly being used in public health. However, the effectiveness of chatbot responses has been debated, and their performance in myopia prevention and control has not been fully explored. This study aimed to evaluate the effectiveness of three well-known chatbots-ChatGPT, Claude, and Bard-in responding to public health questions about myopia. Methods Nineteen public health questions about myopia (including three topics of policy, basics and measures) were responded individually by three chatbots. After shuffling the order, each chatbot response was independently rated by 4 raters for comprehensiveness, accuracy and relevance. Results The study's questions have undergone reliable testing. There was a significant difference among the word count responses of all 3 chatbots. From most to least, the order was ChatGPT, Bard, and Claude. All 3 chatbots had a composite score above 4 out of 5. ChatGPT scored the highest in all aspects of the assessment. However, all chatbots exhibit shortcomings, such as giving fabricated responses. Conclusion Chatbots have shown great potential in public health, with ChatGPT being the best. The future use of chatbots as a public health tool will require rapid development of standards for their use and monitoring, as well as continued research, evaluation and improvement of chatbots.
Collapse
Affiliation(s)
- Yan Wang
- Department of Child and Adolescent Health, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Lihua Liang
- Primary and Secondary School Health Center, Zhengzhou Education Science Planning and Evaluation Center, Zhengzhou Municipal Education Bureau, Zhengzhou, Henan, People’s Republic of China
| | - Ran Li
- Primary and Secondary School Health Center, Zhengzhou Education Science Planning and Evaluation Center, Zhengzhou Municipal Education Bureau, Zhengzhou, Henan, People’s Republic of China
| | - Yihua Wang
- Institute of Science and Technology Information, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Changfu Hao
- Department of Child and Adolescent Health, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| |
Collapse
|
3
|
Almudarris BA, Poonia PS, Mansuri AH, Almalki SA, Gupta S, Mohanty R, Makkad RS. Assessment of Patient Satisfaction and Oral Health-Related Quality of Life Following Full Mouth Rehabilitation with Implant-Supported Prostheses. JOURNAL OF PHARMACY AND BIOALLIED SCIENCES 2024; 16:S2143-S2145. [PMID: 39346489 PMCID: PMC11426675 DOI: 10.4103/jpbs.jpbs_119_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 10/01/2024] Open
Abstract
Background The concept of success is typically established by the researcher or the practitioner rather than the patient, who has the greatest stake in the outcome of the prosthodontics therapy. Aim To assess patient satisfaction and oral health-related quality of life (OHRQoL) in following full mouth rehabilitation with implant-supported prostheses (ISP). Methods and Materials Thirty-two patients who underwent full mouth rehabilitation with ISP were included in this study. The Oral Health Impact Profile-14 (OHIP-14) questionnaire was used for the assessment of patient satisfaction and OHRQoL following full mouth rehabilitation with ISP. Results The functional limitation among study participants before, 1 month, and 3 months after ISP was 2.1 ± 1.3, 1.5 ± 0.8, and 1.4 ± 0.9, respectively. There was a significant reduction in functional limitation, psychological disability, and social disability before and 3 months after ISP. Conclusion There is a significant improvement in patient satisfaction and OHRQoL in following full mouth rehabilitation with ISP.
Collapse
Affiliation(s)
- Ban A. Almudarris
- College of Dentistry, City University Ajman, Ajman, United Arab Emirates
| | - Pooja S. Poonia
- Department of Prosthodontics and Crown and Bridge and Oral Implantology, Ahmedabad Dental College and Hospital, Gujarat, India
| | - Atik H. Mansuri
- Department of Prosthodontics and Dental Materials, Siddhpur Government Dental College, Patan, Gujarat, India
| | - Sultan A. Almalki
- Department of Preventive Dental Sciences, College of Dentistry, Prince Sattam Bin AbdulAziz University, Al-Kharj, Saudi Arabia
| | - Shekhar Gupta
- Department of Prosthodontic Dental Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Rajat Mohanty
- Department of Oral and Maxillofacial Surgery, Kalinga Institute of Dental Sciences, Kalinga Institute of Industrial Technology, KIIT Deemed to be University, Bhubaneswar, Odisha, India
| | - Ramanpal S. Makkad
- Department of Oral Medicine and Radiology, New Horizon Dental College and Research Institute, Sakri, Bilaspur, Chhattisgarh, India
| |
Collapse
|
4
|
Temsah MH, Alhuzaimi AN, Almansour M, Aljamaan F, Alhasan K, Batarfi MA, Altamimi I, Alharbi A, Alsuhaibani AA, Alwakeel L, Alzahrani AA, Alsulaim KB, Jamal A, Khayat A, Alghamdi MH, Halwani R, Khan MK, Al-Eyadhy A, Nazer R. Art or Artifact: Evaluating the Accuracy, Appeal, and Educational Value of AI-Generated Imagery in DALL·E 3 for Illustrating Congenital Heart Diseases. J Med Syst 2024; 48:54. [PMID: 38780839 DOI: 10.1007/s10916-024-02072-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Artificial Intelligence (AI), particularly AI-Generated Imagery, has the potential to impact medical and patient education. This research explores the use of AI-generated imagery, from text-to-images, in medical education, focusing on congenital heart diseases (CHD). Utilizing ChatGPT's DALL·E 3, the research aims to assess the accuracy and educational value of AI-created images for 20 common CHDs. In this study, we utilized DALL·E 3 to generate a comprehensive set of 110 images, comprising ten images depicting the normal human heart and five images for each of the 20 common CHDs. The generated images were evaluated by a diverse group of 33 healthcare professionals. This cohort included cardiology experts, pediatricians, non-pediatric faculty members, trainees (medical students, interns, pediatric residents), and pediatric nurses. Utilizing a structured framework, these professionals assessed each image for anatomical accuracy, the usefulness of in-picture text, its appeal to medical professionals, and the image's potential applicability in medical presentations. Each item was assessed on a Likert scale of three. The assessments produced a total of 3630 images' assessments. Most AI-generated cardiac images were rated poorly as follows: 80.8% of images were rated as anatomically incorrect or fabricated, 85.2% rated to have incorrect text labels, 78.1% rated as not usable for medical education. The nurses and medical interns were found to have a more positive perception about the AI-generated cardiac images compared to the faculty members, pediatricians, and cardiology experts. Complex congenital anomalies were found to be significantly more predicted to anatomical fabrication compared to simple cardiac anomalies. There were significant challenges identified in image generation. Based on our findings, we recommend a vigilant approach towards the use of AI-generated imagery in medical education at present, underscoring the imperative for thorough validation and the importance of collaboration across disciplines. While we advise against its immediate integration until further validations are conducted, the study advocates for future AI-models to be fine-tuned with accurate medical data, enhancing their reliability and educational utility.
Collapse
Affiliation(s)
- Mohamad-Hani Temsah
- College of Medicine, King Saud University, Riyadh, Saudi Arabia.
- Pediatric Department, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia.
- Evidence-Based Health Care & Knowledge Translation Research Chair, Family & Community Medicine Department, College of Medicine, King Saud University, 11362, Riyadh, Saudi Arabia.
| | - Abdullah N Alhuzaimi
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Division of Pediatric Cardiology, Cardiac Science Department, College of Medicine, King Saud University Medical City, 11362, Riyadh, Saudi Arabia
| | - Mohammed Almansour
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Department of Medical Education, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Fadi Aljamaan
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Critical Care Department, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Khalid Alhasan
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Pediatric Department, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
- Kidney & Pancreas Health Center, Organ Transplant Center of Excellence, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Munirah A Batarfi
- Basic Medical Sciences, College of Medicine King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | | | - Amani Alharbi
- Pediatric Department, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | | | - Leena Alwakeel
- Pediatric Department, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Amr Jamal
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Evidence-Based Health Care & Knowledge Translation Research Chair, Family & Community Medicine Department, College of Medicine, King Saud University, 11362, Riyadh, Saudi Arabia
- Department of Family and Community Medicine, King Saud University Medical City, 11362, Riyadh, Saudi Arabia
| | - Afnan Khayat
- Health Information Management Department, Prince Sultan Military College of Health Sciences, Al Dhahran, Saudi Arabia
| | - Mohammed Hussien Alghamdi
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Division of Pediatric Cardiology, Cardiac Science Department, College of Medicine, King Saud University Medical City, 11362, Riyadh, Saudi Arabia
- Department of Medical Education, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Rabih Halwani
- Department of Clinical Sciences, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Muhammad Khurram Khan
- Center of Excellence in Information Assurance, King Saud University, 11653, Riyadh, Saudi Arabia
| | - Ayman Al-Eyadhy
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Pediatric Department, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Rakan Nazer
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Department of Cardiac Science, King Fahad Cardiac Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
5
|
Chattopadhyay J, Deb A, Sharma K, Nawaid KA, Gandhi R, Joshi P, Makkad RS. Creating and Testing a New Computer Vision System for Detecting Dental Problems in Orthodontic Patients. JOURNAL OF PHARMACY AND BIOALLIED SCIENCES 2024; 16:S466-S468. [PMID: 38595489 PMCID: PMC11001109 DOI: 10.4103/jpbs.jpbs_752_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 08/29/2023] [Accepted: 09/03/2023] [Indexed: 04/11/2024] Open
Abstract
Aim The research project focuses on the creation and assessment of an innovative computer vision system designed to identify dental irregularities in individuals undergoing orthodontic treatment. Materials and Methods To establish the computer vision system, a comprehensive dataset of dental images was collected, encompassing various orthodontic cases. The system's algorithm was trained to recognize patterns indicative of common dental anomalies, such as malocclusions, spacing issues, and misalignments. Rigorous testing and refinement of the algorithm were conducted to enhance its accuracy and reliability. Results The validation of the system was carried out using the dental records and images of the 40 patients. The computer vision system's performance was evaluated against assessments made by experienced orthodontists. The results demonstrated a commendable level of concurrence between the system's automated detections and the orthodontists' evaluations, suggesting its potential as a valuable diagnostic tool. Conclusion In conclusion, the development and validation of this novel computer vision system exhibit promising outcomes in its ability to automatically detect dental anomalies in orthodontic patients.
Collapse
Affiliation(s)
- Jnananjan Chattopadhyay
- Department of Dentistry, Murshidabad Medical College, Berhampore, Murshidabad, West Bengal, India
| | - Anamika Deb
- Department of Oral and Maxillofacial Pathology and Microbiology and Forensic Odontology, Bhabha College of Dental Sciences, Bhopal, Madhya Pradesh, India
| | - Kanchan Sharma
- Department of Orthodontics and Dentofacial Orthopedics, Awadh Dental College and Hospital, Jamshedpur, Jharkhand, India
| | - Khwaja Ahmad Nawaid
- Department of Pediatrics and Preventive Dentistry, Mithila Minority Dental College, Darbhanga, Bihar, India
| | - Rachana Gandhi
- Department of Dentistry, GMERS Medical College and Hospital, Himatnagar, Gujarat, India
| | - Poonam Joshi
- Department of Conservative Dentistry and Endodontics, Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, India
| | - Ramanpal Singh Makkad
- Department of Oral Medicine and Radiology, New Horizon Dental College and Research Institute, Sakri, Bilaspur, Chhattisgarh, India
| |
Collapse
|
6
|
Tiwari A, Ghosh A, Agrawal PK, Reddy A, Singla D, Mehta DN, Girdhar G, Paiwal K. Artificial intelligence in oral health surveillance among under-served communities. Bioinformation 2023; 19:1329-1335. [PMID: 38415032 PMCID: PMC10895529 DOI: 10.6026/973206300191329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/31/2023] [Accepted: 12/31/2023] [Indexed: 02/29/2024] Open
Abstract
A sizable percentage of the population in India still does not have easy access to dental facilities. Therefore, it is of interest to document the role of artificial intelligence (AI) in oral surveillance of underserved communities. Available data shows that AI makes it possible to screen, diagnose, track, prioritize, and monitor dental patients remotely via smart devices. As a result, dentists won't have to deal with simple situations that only require standard treatments; freeing them up to focus on more complicated cases. Additionally, this would allow dentists to reach a broader, more underprivileged population in difficult-to-reach places. AI fracture recognition and categorization performance has shown promise in preliminary testing. Methods for detecting aberrations are frequently employed in public health practise and research continues to be focused on them.
Collapse
Affiliation(s)
- Anushree Tiwari
- Clinical Quality and Value, American Academy of Orthopaedic Surgeons, Rosemont, USA
| | - Anirbhan Ghosh
- Department of Orthodontics and Dentofacial Orthopedics, Bhabha College of Dental Sciences, Bhopal, M.P., India
| | - Pankaj Kumar Agrawal
- Department of Oral Pathology and Microbiology, Maitri College of Dentistry and Research Centre, Anjora, Durg, Chhattisgarh, India
| | - Arjun Reddy
- Manipal College of Dental Sciences, Manipal, India
| | - Deepika Singla
- Department of Conservative Dentistry and Endodontics, Desh Bhagat Dental College and Hospital, Malout, India
| | - Dhaval Niranjan Mehta
- Department of Oral Medicine and Radiology, Narsinbhai Patel Dental College and Hospital, Sankalchand Patel University, Visnagar, Gujarat, India
| | - Gaurav Girdhar
- Department of Periodontology, Karnavati School of Dentistry Karnavati University, Gandhinagar, Gujarat, India
| | - Kapil Paiwal
- Department of Oral and Maxillofacial Pathology, Daswani Dental College and Research Center, Kota, Rajasthan, India
| |
Collapse
|
7
|
Agrawal A, Keerthipati S, Sreerama S, Singla D, Acharya S, Mehta D, Kumar S, Paiwal K. Effect of herbal mouthrinsein dental ultrasonic scalers among Indians. Bioinformation 2023; 19:1104-1110. [PMID: 38046514 PMCID: PMC10692984 DOI: 10.6026/973206300191104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/05/2023] Open
Abstract
The use of herbal mouthrinse is gaining momentum in recent years. Therefore, it is of interest to evaluate the effect of 2 herbal mouthrinse (curcumin, cinnamon) in comparison with2 conventional mouthrinse (povidone iodine, chlorhexidine) when used as coolant in dental ultrasonic scalers. Hence, 200 participants were included in this study. Analysis of gingival index, periodontal index at baseline and one month follow up was completed. The inhibitory effects of both conventional and herbal mouth rinse in gingival health are similar. However, cinnamon and curcumin owing to its minimal adverse effects and low cost is useful as an alternative to chlorhexidine for reducing bacterial load in dental aerosols produced due to ultrasonic scalers.
Collapse
Affiliation(s)
- Ankita Agrawal
- Department of Conservative and Endodontics, Buddha Institute of Dental Sciences and Hospital, Patna, Bihar, India
| | - Shilpa Keerthipati
- Department of Orthodontics, Gitam Dental College and Hospital, Visakhapatnam, India
| | | | - Deepika Singla
- Department of Conservative Dentistry & Endodontics, Desh Bhagat Dental College & Hospital, Mandi Gobindgarh, Punjab, India
| | - Sonu Acharya
- Department of Pediatric and Preventive Dentistry, Institute of Dental Sciences, Siksha Anusandhan (Deemed to be) University, Bhubaneswar, India
| | - DhavalNiranjan Mehta
- Department of Oral Medicine and Radiology, Narsinbhai Patel Dental College and Hospital, Sankalchand PatelUniversity, Visnagar, Gujarat, India
| | - Santosh Kumar
- Department of Periodontology, Karnavati School of Dentistry, Karnavati University, Gandhinagar, Gujarat, India
| | - Kapil Paiwal
- Department of Oral & Maxillofacial Pathology, Daswani Dental College & Research Center, Kota, India
| |
Collapse
|
8
|
Zhao K, Farrell K, Mashiku M, Abay D, Tang K, Oberste MS, Burns CC. A search-based geographic metadata curation pipeline to refine sequencing institution information and support public health. Front Public Health 2023; 11:1254976. [PMID: 38035280 PMCID: PMC10683794 DOI: 10.3389/fpubh.2023.1254976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
Background The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) has amassed a vast reservoir of genetic data since its inception in 2007. These public data hold immense potential for supporting pathogen surveillance and control. However, the lack of standardized metadata and inconsistent submission practices in SRA may impede the data's utility in public health. Methods To address this issue, we introduce the Search-based Geographic Metadata Curation (SGMC) pipeline. SGMC utilized Python and web scraping to extract geographic data of sequencing institutions from NCBI SRA in the Cloud and its website. It then harnessed ChatGPT to refine the sequencing institution and location assignments. To illustrate the pipeline's utility, we examined the geographic distribution of the sequencing institutions and their countries relevant to polio eradication and categorized them. Results SGMC successfully identified 7,649 sequencing institutions and their global locations from a random selection of 2,321,044 SRA accessions. These institutions were distributed across 97 countries, with strong representation in the United States, the United Kingdom and China. However, there was a lack of data from African, Central Asian, and Central American countries, indicating potential disparities in sequencing capabilities. Comparison with manually curated data for U.S. institutions reveals SGMC's accuracy rates of 94.8% for institutions, 93.1% for countries, and 74.5% for geographic coordinates. Conclusion SGMC may represent a novel approach using a generative AI model to enhance geographic data (country and institution assignments) for large numbers of samples within SRA datasets. This information can be utilized to bolster public health endeavors.
Collapse
Affiliation(s)
- Kun Zhao
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Katie Farrell
- Cherokee Nation Businesses, Contracting Agency to the Division of Viral Diseases, Centers for Disease Control and Prevention, Catoosa, OK, United States
| | - Melchizedek Mashiku
- Cherokee Nation Businesses, Contracting Agency to the Division of Viral Diseases, Centers for Disease Control and Prevention, Catoosa, OK, United States
| | - Dawit Abay
- Cherokee Nation Businesses, Contracting Agency to the Division of Viral Diseases, Centers for Disease Control and Prevention, Catoosa, OK, United States
| | - Kevin Tang
- Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - M Steven Oberste
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Cara C Burns
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| |
Collapse
|