Development of phenotype algorithms using electronic medical records and incorporating natural language processing

被引：202

作者：

Liao, Katherine P. ^{[1
,2
]}

Cai, Tianxi ^{[3
]}

Savova, Guergana K. ^{[4
]}

Murphy, Shawn N. ^{[5
]}

Karlson, Elizabeth W. ^{[1
,2
]}

Ananthakrishnan, Ashwin N. ^{[6
]}

Gainer, Vivian S. ^{[7
]}

Shaw, Stanley Y. ^{[2
,8
]}

Xia, Zongqi ^{[2
,9
]}

Szolovits, Peter ^{[10
]}

Churchill, Susanne ^{[2
]}

Kohane, Isaac ^{[2
,5
]}

机构：

[1] Brigham & Womens Hosp, Div Rheumatol Immunol & Allergy, Boston, MA 02115 USA

[2] Harvard Univ, Sch Med, Boston, MA USA

[3] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA

[4] Childrens Hosp Boston, Dept Pediat, Boston, MA USA

[5] Massachusetts Gen Hosp, Dept Neurol, Boston, MA 02114 USA

[6] Massachusetts Gen Hosp, Dept Gastroenterol, MGH Crohns & Colitis Ctr, Boston, MA 02114 USA

[7] Partners HealthCare Syst, Partners Res Comp, Boston, MA USA

[8] Massachusetts Gen Hosp, Ctr Syst Biol, Boston, MA 02114 USA

[9] Harvard Univ, Sch Med, Dept Neurol, Boston, MA 02115 USA

[10] MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA

来源：

BMJ-BRITISH MEDICAL JOURNAL | 2015年 / 350卷

基金：

美国国家卫生研究院;

关键词：

RHEUMATOID-ARTHRITIS; ULCERATIVE-COLITIS; DISCOVERY RESEARCH; CROHNS-DISEASE; NORMALIZATION; RISK; IDENTIFICATION; PREVALENCE; SYSTEM;

D O I：

10.1136/bmj.h1885

中图分类号：

R5 [内科学];

学科分类号：

1002 ; 100201 ;

摘要：

Electronic medical records are emerging as a major source of data for clinical and translational research studies, although phenotypes of interest need to be accurately defined first. This article provides an overview of how to develop a phenotype algorithm from electronic medical records, incorporating modern informatics and biostatistics methods. © BMJ Publishing Group Ltd 2015.

引用

页数：6

共 35 条

[1] Thromboprophylaxis Is Associated With Reduced Post-hospitalization Venous Thromboembolic Events in Patients With Inflammatory Bowel Diseases [J].

Ananthakrishnan, Ashwin N. ;

Cagan, Andrew ;

Gainer, Vivian S. ;

Cheng, Su-Chun ;

Cai, Tianxi ;

Scoville, Elizabeth ;

Konijeti, Gauree G. ;

Szolovits, Peter ;

Shaw, Stanley Y. ;

Churchill, Susanne ;

Karlson, Elizabeth W. ;

Murphy, Shawn N. ;

Kohane, Isaac ;

Liao, Katherine P. .

CLINICAL GASTROENTEROLOGY AND HEPATOLOGY, 2014, 12 (11) :1905-1910

[2] Improving Case Definition of Crohn's Disease and Ulcerative Colitis in Electronic Medical Records Using Natural Language Processing: A Novel Informatics Approach [J].

Ananthakrishnan, Ashwin N. ;

Cai, Tianxi ;

Savova, Guergana ;

Cheng, Su-Chun ;

Chen, Pei ;

Perez, Raul Guzman ;

Gainer, Vivian S. ;

Murphy, Shawn N. ;

Szolovits, Peter ;

Xia, Zongqi ;

Shaw, Stanley ;

Churchill, Susanne ;

Karlson, Elizabeth W. ;

Kohane, Isaac ;

Plenge, Robert M. ;

Liao, Katherine P. .

INFLAMMATORY BOWEL DISEASES, 2013, 19 (07) :1411-1420

[3]

Ananthakrishnan AN, 2013, INFLAMM BOWEL DIS, V19, P37, DOI [10.1002/ibd.22951, 10.1097/MIB.0b013e3182902ad9]

[4] An overview of MetaMap: historical perspective and recent advances [J].

Aronson, Alan R. ;

Lang, Francois-Michel .

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION, 2010, 17 (03) :229-236

[5] Exploring semantic groups through visual approaches [J].

Bodenreider, O ;

McCray, AT .

JOURNAL OF BIOMEDICAL INFORMATICS, 2003, 36 (06) :414-432

[6] Rapid Identification of Myocardial Infarction Risk Associated With Diabetes Medications Using Electronic Medical Records [J].

Brownstein, John S. ;

Murphy, Shawn N. ;

Goldfine, Allison B. ;

Grant, Richard W. ;

Sordo, Margarita ;

Gainer, Vivian ;

Colecchi, Judith A. ;

Dubey, Anil ;

Nathan, David M. ;

Glaser, John P. ;

Kohane, Isaac S. .

DIABETES CARE, 2010, 33 (03) :526-531

[7] Using Natural Language Processing to Improve Efficiency of Manual Chart Abstraction in Research: The Case of Breast Cancer Recurrence [J].

Carrell, David S. ;

Halgrim, Scott ;

Diem-Thy Tran ;

Buist, Diana S. M. ;

Chubak, Jessica ;

Chapman, Wendy W. ;

Savova, Guergana .

AMERICAN JOURNAL OF EPIDEMIOLOGY, 2014, 179 (06) :749-758

[8] Portability of an algorithm to identify rheumatoid arthritis in electronic health records [J].

Carroll, Robert J. ;

Thompson, Will K. ;

Eyler, Anne E. ;

Mandelin, Arthur M. ;

Cai, Tianxi ;

Zink, Raquel M. ;

Pacheco, Jennifer A. ;

Boomershine, Chad S. ;

Lasko, Thomas A. ;

Xu, Hua ;

Karlson, Elizabeth W. ;

Perez, Raul G. ;

Gainer, Vivian S. ;

Murphy, Shawn N. ;

Ruderman, Eric M. ;

Pope, Richard M. ;

Plenge, Robert M. ;

Kho, Abel Ngo ;

Liao, Katherine P. ;

Denny, Joshua C. .

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION, 2012, 19 (E1) :E162-E169

[9] PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations [J].

Denny, Joshua C. ;

Ritchie, Marylyn D. ;

Basford, Melissa A. ;

Pulley, Jill M. ;

Bastarache, Lisa ;

Brown-Gentry, Kristin ;

Wang, Deede ;

Masys, Dan R. ;

Roden, Dan M. ;

Crawford, Dana C. .

BIOINFORMATICS, 2010, 26 (09) :1205-1210

[10]

Endicott M, 2012, J AHIMA, V82, P60

← 1 2 3 4 →