Ontologizing health systems data at scale: making translational discovery a reality

被引：8

作者：

Callahan, Tiffany J. ^{[1
,2
]}

Stefanski, Adrianne L. ^{[1
]}

Wyrwa, Jordan M. ^{[3
]}

Zeng, Chenjie ^{[4
]}

Ostropolets, Anna ^{[2
]}

Banda, Juan M. ^{[5
]}

Baumgartner, William A., Jr. ^{[1
]}

Boyce, Richard D. ^{[6
]}

Casiraghi, Elena ^{[7
,8
]}

Coleman, Ben D. ^{[8
]}

Collins, Janine H. ^{[9
]}

Davies, Sara J. Deakyne ^{[10
]}

Feinstein, James A.

Lin, Asiyah Y. ^{[4
]}

Martin, Blake ^{[11
]}

Matentzoglu, Nicolas A.

Meeker, Daniella

Reese, Justin

Sinclair, Jessica

Taneja, Sanya B.

Trinkley, Katy E.

Vasilevsky, Nicole A.

Williams, Andrew E.

Zhang, Xingmin A. ^{[8
]}

Denny, Joshua C. ^{[4
]}

Ryan, Patrick B.

Hripcsak, George ^{[2
]}

Bennett, Tellen D. ^{[11
]}

Haendel, Melissa A. ^{[11
]}

Robinson, Peter N. ^{[8
]}

Hunter, Lawrence E. ^{[1
]}

Kahn, Michael G.

机构：

[1] Univ Colorado, Computat Biosci Program, Anschutz Med Campus, Aurora, CO 80045 USA

[2] Columbia Univ, Dept Biomed Informat, Irving Med Ctr, New York, NY 10032 USA

[3] Univ Colorado, Sch Med, Dept Phys Med & Rehabil, Anschutz Med Campus, Aurora, CO 80045 USA

[4] Natl Human Genome Res Inst, NIH, Bethesda, MD 20892 USA

[5] Georgia State Univ, Dept Comp Sci, Atlanta, GA 30303 USA

[6] Univ Pittsburgh, Dept Biomed Informat, Sch Med, Pittsburgh, PA 15260 USA

[7] Univ Milan, Comp Sci, Milan, Italy

[8] Jackson Lab Genom Med, Farmington, CT 06032 USA

[9] Univ Cambridge, Dept Haematol, Cambridge, England

[10] Childrens Hosp Colorado, Analyt Resource Ctr, Dept Res Informat & Data Sci, Aurora, CO 80045 USA

[11] Univ Colorado, Dept Pediat, Sch Med, Aurora, CO 80045 USA

来源：

NPJ DIGITAL MEDICINE | 2023年 / 6卷 / 01期

基金：

英国医学研究理事会;

关键词：

HIGH-THROUGHPUT; DEEP; CLASSIFICATION; REPRESENTATION; STANDARD; LOINC; TOOL;

D O I：

10.1038/s41746-023-00830-x

中图分类号：

R19 [保健组织与事业（卫生事业管理）];

学科分类号：

摘要：

Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68-99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.

引用

页数：18

共 122 条

[1]

Aaron Z. X., 2020, LOINC2HPO ANNOTATION

[2] HITECH Act Drove Large Gains In Hospital Electronic Health Record Adoption [J].

Adler-Milstein, Julia ;

Jha, Ashish K. .

HEALTH AFFAIRS, 2017, 36 (08) :1416-1422

[3] SMART on FHIR Genomics: facilitating standardized clinico-genomic apps [J].

Alterovitz, Gil ;

Warner, Jeremy ;

Zhang, Peijin ;

Chen, Yishen ;

Ullman-Cullere, Mollie ;

Kreda, David ;

Kohane, Isaac S. .

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION, 2015, 22 (06) :1173-1178

[4] Assessing the practice of biomedical ontology evaluation: Gaps and opportunities [J].

Amith, Muhammad ;

He, Zhe ;

Bian, Jiang ;

Lossio-Ventura, Juan Antonio ;

Tao, Cui .

JOURNAL OF BIOMEDICAL INFORMATICS, 2018, 80 :1-13

[5] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[6] The Digitization of Patient Care: A Review of the Effects of Electronic Health Records on Health Care Quality and Utilization [J].

Atasoy, Hilal ;

Greenwood, Brad N. ;

McCullough, Jeffrey Scott .

ANNUAL REVIEW OF PUBLIC HEALTH, VOL 40, 2019, 40 :487-500

[7]

Banda J. M., 2020, OHDSI ANANKE A TOOL

[8] An ontology for cell types [J].

Bard, J ;

Rhee, SY ;

Ashburner, M .

GENOME BIOLOGY, 2005, 6 (02)

[9] Informatics and machine learning to define the phenotype [J].

Basile, Anna Okula ;

Ritchie, Marylyn DeRiggi .

EXPERT REVIEW OF MOLECULAR DIAGNOSTICS, 2018, 18 (03) :219-226

[10] Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease [J].

Bastarache, Lisa ;

Hughey, Jacob J. ;

Goldstein, Jeffrey A. ;

Bastraache, Julie A. ;

Das, Satya ;

Zaki, Neil Charles ;

Zeng, Chenjie ;

Tang, Leigh Anne ;

Roden, Dan M. ;

Denny, Joshua C. .

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION, 2019, 26 (12) :1437-1447

← 1 2 3 4 5 6 7 8 9 10 →