titipata / affiliation_parser

Simple python parser for MEDLINE, Pubmed OA affiliation string
37 stars 15 forks source link

multiple affiliation in one affiliation text #23

Open Lix1993 opened 2 years ago

Lix1993 commented 2 years ago
from affiliation_parser import parse_affil

affil_text = "Department of gynecology and obstetrics, university hospital of South Reunion Island, BP 350, 97448 Saint-Pierre cedex, Reunion; Faculty of medicine, university of Reunion, 97490 St-Denis, Reunion; CEPOI, perinatal center of study of the Indian ocean, faculty of medicine, university hospital of South Reunion Island, St-Pierre 97448, Reunion."

parse_affil(affil_text)

{'full_text': 'Department of gynecology and obstetrics, university hospital of South Reunion Island, BP 350,  Saint-Pierre cedex, Reunion Faculty of medicine, university of Reunion, 97490 St-Denis, Reunion CEPOI, perinatal center of study of the Indian ocean, faculty of medicine, university hospital of South Reunion Island, St-Pierre , Reunion.',
 'department': 'Department of gynecology and obstetrics, Reunion Faculty of medicine, faculty of medicine',
 'institution': 'university hospital of South Reunion Island, university of Reunion',
 'email': '',
 'zipcode': '97448',
 'location': '97490 St-Denis, Reunion CEPOI, perinatal center of study of the Indian ocean, university hospital of South Reunion Island, St-Pierre , Reunion',
 'country': ''}
Lix1993 commented 2 years ago

there are 3 institutions, this should return None.

titipata commented 2 years ago

Thanks @Lix1993. I will take a look later on! They typically have semicolon separating the affiliation. Maybe we could separate it and return a list of parsed affiliations instead?

Lix1993 commented 2 years ago

well , it will has no ;,

an example:

Digestive Pathophysiology unit, Baggiovara Hospital, Modena, italy. Department of Medical and Surgical Sciences, university of Bologna, Bologna, italy. Department of Surgery, General and Bariatric Surgery unit, 2nd university of Naples, Napoli, italy. Department of Translational Research and New Technology in Medicine and Surgery, university of Pisa, Pisa, italy. Gastroenterology unit, Department of internal Medicine, university of Genoa, Genova, italy. Gastroenterology unit, Department of Surgery, Oncology and Gastroenterology, university of Padua, Padova, italy.
Lix1993 commented 2 years ago

affiliation text may has many peaple's affil due to historical reasion an example:

K. Toupin-April, PhD, Associate Scientist, Children's Hospital of Eastern Ontario Research Institute, and Assistant Professor, Department of Pediatrics and School of Rehabilitation Sciences, University of Ottawa; J. Barton, MD, VA Portland Health Care System, and Associate Professor, Oregon Health and Science University; L. Fraenkel, MD, Professor of Medicine, Department of Internal Medicine, Yale University; L.C. Li, PT, PhD, Professor, Department of Physical Therapy, University of British Columbia, and Senior Scientist, Arthritis Research Centre of Canada; P. Brooks, MD, Professor, School of Population and Global Health, University of Melbourne; M. De Wit, PhD, Patient Research Partner, VU Medical Centre; D. Stacey, RN, PhD, Full Professor, School of Nursing, University of Ottawa, and Senior Scientist, The Ottawa Hospital Research Institute; F. Légaré, MD, PhD, Full Professor, Department of Family Medicine and Emergency Medicine, Université Laval; A. Meara, MD, The Ohio State University; B. Shea, PhD, Clinical Scientist, Bruyère Research Institute, and Senior Methodologist, Ottawa Health Research Institute, and Adjunct Professor, Department of Epidemiology and Community Medicine, University of Ottawa; A. Lyddiatt, Patient Research Partner; C. Hofstetter, Patient Research Partner; L. Gossec, MD, PhD, Sorbonne Universités, UPMC Univ Paris 06, GRC-08, and Pitie-Salpétrière Hospital, AP-HP, Rheumatology Department; R. Christensen, PhD, Professor, Senior Biostatistician, Musculoskeletal Statistics Unit, The Parker Institute, Bispebjerg and Frederiksberg Hospital; M. Scholte-Voshaar, MSc, Patient Research Partner, Department Psychology, Health and Technology, University of Twente; M.E. Suarez-Almazor MD, PhD, Professor, Department of General Internal Medicine, Section of Rheumatology and Clinical Immunology, University of Texas MD Anderson Cancer Center; A. Boonen, MD, PhD, Professor of Rheumatology, Department of Internal Medicine, Division of Rheumatology, Maastricht University Medical Center and Caphri Research Institute, Maastricht University; T. Meade, PhD, Professor, Western Sydney University and Faculty of Medicine, University of Sydney; L. March, MD, Professor, Department of Medicine, University of Sydney, Institute of Bone and Joint Research and Department of Rheumatology, Royal North Shore Hospital; C. Pohl, MD, Rheumatologist, Department of Internal Medicine II Rheumatology, Clinical Immunology, Osteology, Physical Therapy and Sports Medicine, Schlosspark-Klinik, Charité, University Medicine Berlin; J.E. Jull, OT, PhD, Postdoctoral Fellow, Integrated Knowledge Translation Network and University of Ottawa; S. Sivarajah, BSc, Research Assistant, Children's Hospital of Eastern Ontario Research Institute; W. Campbell, LLB, Patient Research Partner; R. Alten, MD, PhD, Professor of Medicine, Head of Department of Internal Medicine II, Director of Rheumatology Research Center, Rheumatology, Clinical Immunology, Osteology, Physical Therapy and Sports Medicine, Schlosspark-Klinik, Charité, University Medicine Berlin; S. Karuranga, MPH, Researcher, Access to Medicine Foundation; E. Morgan, MD, Associate Professor, Division of Rheumatology, Cincinnati Children's Hospital Medical Center; J. Kaufman, BSc, Centre for Health Communication and Participation, School of Psychology and Public Health, La Trobe University; S. Hill, PhD, Centre for Health Communication and Participation, School of Psychology and Public Health, La Trobe University; L.J. Maxwell, PhD, Ottawa Hospital Research Institute, Centre for Practice-Changing Research and University of Ottawa; V. Welch, PhD, Scientist, Bruyère Research Institute, Bruyère Continuing Care and School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa; D. Beaton, PhD, Musculoskeletal Health and Outcomes Research, Li Ka Shing Knowledge Institute, St. Michael's Hospital, and Senior Scientist, Institute for Work and Health, Associate Professor, Institute Health Policy, Management and Evaluation, University of Toronto; Y. El-Miedany, MD, Professor, Rheumatology and Rehabilitation, Ain Shams University, and Honorary Senior Clinical Lecturer, King's College London; P.S. Tugwell, MD, Professor, Department of Medicine, Faculty of Medicine, University of Ottawa, and Senior Scientist, Clinical Epidemiology Program, Ottawa Hospital Research Institute, Department of Epidemiology and Community Medicine, Faculty of Medicine, and Institute of Population Health, Centre for Global Health, University of Ottawa.