Filters








90 Hits in 6.5 sec

CREATE: Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records using OMOP Common Data Model [article]

Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William Hersh, Hongfang Liu
2019 arXiv   pre-print
Methods: In this paper, we present the implementation of Cohort Retrieval Enhanced by Analysis of Text from EHRs (CREATE), a cohort retrieval system that can execute textual cohort selection queries on  ...  Outcomes Partnership (OMOP) Common Data Model (CDM) to enhance model portability.  ...  The work was supported by National Institutes of Health grants R01LM011934, R01EB19403, R01LM11829, and U01TR02062.  ... 
arXiv:1901.07601v1 fatcat:vacjcl23inamlapjlmwizb2clu

On Cohort Retrieval System from Clinical Data Repositories using OMOP Common Data Model: A Proof-of-Concept Implementation (Preprint)

Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William Hersh, Hongfang Liu
2019 JMIR Medical Informatics  
of Text from Electronic Health Records (CREATE).  ...  In this paper, we present the implementation of a cohort retrieval system that can execute textual cohort selection queries on both structured data and unstructured text-Cohort Retrieval Enhanced by Analysis  ...  The work was supported by the National Institutes of Health (grants R01LM011934, R01EB19403, R01LM11829, and U01TR02062).  ... 
doi:10.2196/17376 pmid:33021486 fatcat:jnr452ywrzbuhajeamukcb4aqi

Clinical Predictive Modeling Development and Deployment through FHIR Web Services

Mohammed Khalilia, Myung Choi, Amelia Henderson, Sneha Iyengar, Mark Braunstein, Jimeng Sun
2015 AMIA Annual Symposium Proceedings  
The services enable model development using electronic health records (EHRs) stored in OMOP CDM databases and model deployment for scoring individual patients through FHIR resources.  ...  In this paper we demonstrate a software architecture for developing and deploying clinical predictive models using web services via the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (  ...  Acknowledgment This work was supported by the National Science Foundation, award #1418511, Children's Healthcare of Atlanta, CDC i-SMILE project, Google Faculty Award, AWS Research Award, and Microsoft  ... 
pmid:26958207 pmcid:PMC4765683 fatcat:54qcsk3xs5gbnejegb4zk7a5su

Transformation of Pathology Reports into the Common Data Model with Oncology Module: Use Case for Colon Cancer (Preprint)

Borim Ryu, Eunsil Yoon, Seok Kim, Sejoon Lee, Hyunyoung Baek, Soyoung Yi, Hee Young Na, Ji-Won Kim, Rong-Min Baek, Hee Hwang, Sooyoung Yoo
2020 Journal of Medical Internet Research  
Common data models (CDMs) help standardize electronic health record data and facilitate outcome analysis for observational and longitudinal research.  ...  recommended by the OMOP CDM.  ...  text in electronic health record (EHR) systems.  ... 
doi:10.2196/18526 pmid:33295294 fatcat:4h74phpnivbebefswlbkogsnyq

Feasibility and utility of applications of the common data model to multiple, disparate observational health databases

Erica A Voss, Rupa Makadia, Amy Matcho, Qianli Ma, Chris Knoll, Martijn Schuemie, Frank J DeFalco, Ajit Londhe, Vivienne Zhu, Patrick B Ryan
2015 JAMIA Journal of the American Medical Informatics Association  
Objectives To evaluate the utility of applying the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) across multiple observational databases within an organization and to apply  ...  We developed a standardized analytic tool to replicate the cohort construction process from a published epidemiology protocol and applied the analysis to all 6 databases to assess time-to-execution and  ...  Also, we thank Anton Ivonov and Alexey Arestenko for their programming and data management efforts associated with our OMOP CDMs and OMOP Vocabulary.  ... 
doi:10.1093/jamia/ocu023 pmid:25670757 pmcid:PMC4457111 fatcat:ri27i7xcbjc7ro5muglbp4xaim

Big Dreams With Big Data! Use of Clinical Informatics to Inform Biomarker Discovery

Siddharth Singh
2019 Clinical and Translational Gastroenterology  
Electronic health records form a rich but complex source of large amounts of data gathered during routine clinical care.  ...  In this article, we introduce important building blocks for precision medicine, including common data models, text mining and natural language processing, privacy-preserved record linkage, machine learning  ...  INTRODUCTION Adoption and meaningful use of electronic health records (EHRs) has continued to increase, spurred by federal mandates in the United States.  ... 
doi:10.14309/ctg.0000000000000018 pmid:30908310 pmcid:PMC6445607 fatcat:mgxszelf3vadxhekbrn5hcsiym

Criteria2Query: a natural language interface to clinical databases for cohort definition

Chi Yuan, Patrick B Ryan, Casey Ta, Yixuan Guo, Ziran Li, Jill Hardin, Rupa Makadia, Peng Jin, Ning Shang, Tian Kang, Chunhua Weng
2019 JAMIA Journal of the American Medical Informatics Association  
Data-driven cohort definition is appealing but requires substantial knowledge of terminologies and clinical data models.  ...  Cohort definition is a bottleneck for conducting clinical research and depends on subjective decisions by domain experts.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge the Observational Health Data Sciences and Informatics technical teams for their kind help, particularly Lee Evans.  ... 
doi:10.1093/jamia/ocy178 pmid:30753493 pmcid:PMC6402359 fatcat:5xg4qbkqsbc3vjnr4rvg2dahw4

Representing Knowledge Consistently Across Health Systems

S. T. Rosenbloom, R. J. Carroll, J. L. Warner, M. E. Matheny, J. C. Denny
2017 IMIA Yearbook of Medical Informatics  
Objectives: Electronic health records (EHRs) have increasingly emerged as a powerful source of clinical data that can be leveraged for reuse in research and in modular health apps that integrate into diverse  ...  Method: We reviewed several recent studies covering the knowledge representation in the common data models for the Observational Medical Outcomes Partnership (OMOP) and its Observational Health Data Sciences  ...  Introduction Electronic Health Records (EHRs) have emerged as a powerful tool to facilitate discoveries that can improve health.  ... 
doi:10.1055/s-0037-1606495 fatcat:avdentz3jbhspmg5rql6rt6fge

Representing Knowledge Consistently Across Health Systems

S. T. Rosenbloom, R. J. Carroll, J. L. Warner, M. E. Matheny, J. C. Denny
2017 IMIA Yearbook of Medical Informatics  
Objectives: Electronic health records (EHRs) have increasingly emerged as a powerful source of clinical data that can be leveraged for reuse in research and in modular health apps that integrate into diverse  ...  Method: We reviewed several recent studies covering the knowledge representation in the common data models for the Observational Medical Outcomes Partnership (OMOP) and its Observational Health Data Sciences  ...  Introduction Electronic Health Records (EHRs) have emerged as a powerful tool to facilitate discoveries that can improve health.  ... 
doi:10.15265/iy-2017-018 pmid:29063555 pmcid:PMC6239235 fatcat:4oo5oxmmarhcjaifykqpivwtre

EHDEN - D4.5 - Roadmap for interoperability solutions

Kees Van Bochove, Emma Vos, Maxim Moinat, Sebastiaan Van Sandijk, Tess Korthout, Peyman Mohtashani
2020 Zenodo  
The EHDEN project has explicitly chosen to standardize healthcare data for analysis using the OMOP Common Data Model, but other interoperability solutions, such as i2b2, CDISC, FHIR, openEHR, GA4GH etc  ...  This document addresses the relevance of those standards for the data (re)use goals of EHDEN, and points out how OMOP and OHDSI relate to them.  ...  , including patient electronic health records (EHR), cohort studies and registries and even clinical trial data.  ... 
doi:10.5281/zenodo.4474373 fatcat:3zw4vbrqyvhitc4pgqc2n2wiou

What you need to know before implementing a clinical research data warehouse: a comparative review of integrated data repositories in health care institutions (Preprint)

Kristina K Gagalova, M. Angelica Leon Elizalde, Elodie Portales-Casamar, Matthias Görges
2020 JMIR Formative Research  
We identified 4 common architecture models that use different approaches for data processing and integration.  ...  IDR implementations are diverse and complex undertakings, which benefit from being preceded by an evaluation of requirements and definition of scope in the early planning stage.  ...  Acknowledgments The project was supported, in part, by an Evidence to Innovation (E2i) Research Theme seed grant through the BC Children's Hospital Research Institute.  ... 
doi:10.2196/17687 pmid:32852280 fatcat:q3luq63hgvds3n5kodxspltuyy

Test collections for electronic health record-based clinical information retrieval

Yanshan Wang, Andrew Wen, Sijia Liu, William Hersh, Steven Bedrick, Hongfang Liu
2019 JAMIA Open  
Electronic health record (EHR) data, including structured and free-text data, from 45 000 patients who are a part of the Mayo Clinic Biobank cohort was retrieved from the clinical data warehouse.  ...  We described the creation of test collections, including a to-be-evaluated document pool using five retrieval models, and human assessment guidelines.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/jamiaopen/ooz016 pmid:31709390 pmcid:PMC6824517 fatcat:n5dldhkybvfanjktk42yfdyipq

An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C) [article]

Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert Miller, Andrew Williams, Daniel Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-el-rub, Dalton Schutte (+17 others)
2022 arXiv   pre-print
The corpora were derived from texts from three different institutions (Mayo Clinic, University of Kentucky, University of Minnesota).  ...  The study as a consortium effort of the N3C NLP subgroup demonstrates the feasibility of creating a federated NLP algorithm development and benchmarking platform to enhance multi-institution clinical NLP  ...  Introduction Over the past decade, Electronic Health Record (EHR) systems have been increasingly implemented at US healthcare institutions.  ... 
arXiv:2110.10780v3 fatcat:pauori3y6nhy5g6nrj2k3pvg2u

A new paradigm for accelerating clinical data science at Stanford Medicine [article]

Somalee Datta, Jose Posada, Garrick Olson, Wencheng Li, Ciaran O'Reilly, Deepa Balraj, Joseph Mesterhazy, Joseph Pallas, Priyamvada Desai, Nigam Shah
2020 arXiv   pre-print
Furthermore, the data is standardized such that analysis done at Stanford can be replicated elsewhere using the same analytical code and clinical concepts.  ...  However, the traditional data warehouse and Honest Broker approaches that are in current use, are not scalable.  ...  of 18 We thank Nigam Shah's lab for being early adopters of the dataset, and tools and providing us with feedback and support.  ... 
arXiv:2003.10534v1 fatcat:mbsbmigcrjhxtazfsqlrlvkmju

Privacy-protecting, reliable response data discovery using COVID-19 patient observations

Jihoon Kim, Larissa Neumann, Paulina Paul, Michele E Day, Michael Aratow, Douglas S Bell, Jason N Doctor, Ludwig C Hinske, Xiaoqian Jiang, Katherine K Kim, Michael E Matheny, Daniella Meeker (+7 others)
2021 JAMIA Journal of the American Medical Informatics Association  
To utilize, in an individual and institutional privacy-preserving manner, electronic health record (EHR) data from 202 hospitals by analyzing answers to COVID-19-related questions and posting these answers  ...  We demonstrated that it is possible to answer questions about COVID-19 using EHR data from systems that have different policies and must follow various regulations, without moving data out of their health  ...  All sites have transformed or are actively transforming data into the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM), but some of them only use data from COVID-19 registry patients  ... 
doi:10.1093/jamia/ocab054 pmid:34051088 pmcid:PMC8194878 fatcat:s4yv2ngnfze73hdux5twulhkxy
« Previous Showing results 1 — 15 out of 90 results