1
|
Brunette CA, Yi T, Danowski ME, Cardellino M, Harrison A, Assimes TL, Knowles JW, Christensen KD, Sturm AC, Sun YV, Hui Q, Pyarajan S, Shi Y, Whitbourne SB, Gaziano JM, Muralidhar S, Vassy JL. Development and utility of a clinical research informatics application for participant recruitment and workflow management for a return of results pilot trial in familial hypercholesterolemia in the Million Veteran Program. JAMIA Open 2024; 7:ooae020. [PMID: 38464744 PMCID: PMC10923213 DOI: 10.1093/jamiaopen/ooae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/26/2023] [Accepted: 02/14/2024] [Indexed: 03/12/2024] Open
Abstract
Objective The development of clinical research informatics tools and workflow processes associated with re-engaging biobank participants has become necessary as genomic repositories increasingly consider the return of actionable research results. Materials and Methods Here we describe the development and utility of an informatics application for participant recruitment and enrollment management for the Veterans Affairs Million Veteran Program Return Of Actionable Results Study, a randomized controlled pilot trial returning individual genetic results associated with familial hypercholesterolemia. Results The application is developed in Python-Flask and was placed into production in November 2021. The application includes modules for chart review, medication reconciliation, participant contact and biospecimen logging, survey recording, randomization, and documentation of genetic counseling and result disclosure. Three primary users, a genetic counselor and two research coordinators, and 326 Veteran participants have been integrated into the system as of February 23, 2023. The application has successfully handled 3367 task requests involving greater than 95 000 structured data points. Specifically, application users have recorded 326 chart reviews, 867 recruitment telephone calls, 158 telephone-based surveys, and 61 return of results genetic counseling sessions, among other available study tasks. Conclusion The development of usable, customizable, and secure informatics tools will become increasingly important as large genomic repositories begin to return research results at scale. Our work provides a proof-of-concept for developing and using such tools to aid in managing the return of results process within a national biobank.
Collapse
Affiliation(s)
- Charles A Brunette
- Veterans Affairs Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Thomas Yi
- Veterans Affairs Boston Healthcare System, Boston, MA, United States
| | - Morgan E Danowski
- Veterans Affairs Boston Healthcare System, Boston, MA, United States
| | - Mark Cardellino
- Veterans Affairs Boston Healthcare System, Boston, MA, United States
| | - Alicia Harrison
- Genetic Counseling Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, United States
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
- Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA, United States
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Joshua W Knowles
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
- Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA, United States
- Family Heart Foundation, Pasadena, CA, United States
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, United States
- Department of Population Medicine, Harvard Medical School, Boston, MA, United States
| | | | - Yan V Sun
- Atlanta VA Health Care System, Decatur, GA, United States
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Qin Hui
- Atlanta VA Health Care System, Decatur, GA, United States
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Saiju Pyarajan
- Veterans Affairs Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Yunling Shi
- Veterans Affairs Boston Healthcare System, Boston, MA, United States
| | - Stacey B Whitbourne
- Veterans Affairs Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Division of Aging, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - J Michael Gaziano
- Veterans Affairs Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Division of Aging, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Sumitra Muralidhar
- Office of Research and Development, Veterans Health Administration, Washington, DC, United States
| | - Jason L Vassy
- Veterans Affairs Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Division of General Internal Medicine and Primary Care, Brigham and Women’s Hospital, Boston, MA, United States
- Population Precision Health, Ariadne Labs, Boston, MA, United States
| |
Collapse
|
2
|
Palchuk MB, London JW, Perez-Rey D, Drebert ZJ, Winer-Jones JP, Thompson CN, Esposito J, Claerhout B. A global federated real-world data and analytics platform for research. JAMIA Open 2023; 6:ooad035. [PMID: 37193038 PMCID: PMC10182857 DOI: 10.1093/jamiaopen/ooad035] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/09/2023] [Accepted: 05/05/2023] [Indexed: 05/18/2023] Open
Abstract
Objective This article describes a scalable, performant, sustainable global network of electronic health record data for biomedical and clinical research. Materials and Methods TriNetX has created a technology platform characterized by a conservative security and governance model that facilitates collaboration and cooperation between industry participants, such as pharmaceutical companies and contract research organizations, and academic and community-based healthcare organizations (HCOs). HCOs participate on the network in return for access to a suite of analytics capabilities, large networks of de-identified data, and more sponsored trial opportunities. Industry participants provide the financial resources to support, expand, and improve the technology platform in return for access to network data, which provides increased efficiencies in clinical trial design and deployment. Results TriNetX is a growing global network, expanding from 55 HCOs and 7 countries in 2017 to over 220 HCOs and 30 countries in 2022. Over 19 000 sponsored clinical trial opportunities have been initiated through the TriNetX network. There have been over 350 peer-reviewed scientific publications based on the network's data. Conclusions The continued growth of the TriNetX network and its yield of clinical trial collaborations and published studies indicates that this academic-industry structure is a safe, proven, sustainable path for building and maintaining research-centric data networks.
Collapse
Affiliation(s)
- Matvey B Palchuk
- Corresponding Author: Matvey B. Palchuk, MD, MS, FAMIA, TriNetX, LLC, 125 Cambridge Park Dr, Suite 500, Cambridge, MA 02140, USA;
| | - Jack W London
- Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - David Perez-Rey
- Biomedical Informatics Group, Artificial Intelligence Department, Universidad Politécnica de Madrid, Madrid, Spain
| | | | | | | | | | | |
Collapse
|
3
|
Zhang H, Lyu T, Yin P, Bost S, He X, Guo Y, Prosperi M, Hogan WR, Bian J. A scoping review of semantic integration of health data and information. Int J Med Inform 2022; 165:104834. [PMID: 35863206 DOI: 10.1016/j.ijmedinf.2022.104834] [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: 03/21/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVE We summarized a decade of new research focusing on semantic data integration (SDI) since 2009, and we aim to: (1) summarize the state-of-art approaches on integrating health data and information; and (2) identify the main gaps and challenges of integrating health data and information from multiple levels and domains. MATERIALS AND METHODS We used PubMed as our focus is applications of SDI in biomedical domains and followed the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) to search and report for relevant studies published between January 1, 2009 and December 31, 2021. We used Covidence-a systematic review management system-to carry out this scoping review. RESULTS The initial search from PubMed resulted in 5,326 articles using the two sets of keywords. We then removed 44 duplicates and 5,282 articles were retained for abstract screening. After abstract screening, we included 246 articles for full-text screening, among which 87 articles were deemed eligible for full-text extraction. We summarized the 87 articles from four aspects: (1) methods for the global schema; (2) data integration strategies (i.e., federated system vs. data warehousing); (3) the sources of the data; and (4) downstream applications. CONCLUSION SDI approach can effectively resolve the semantic heterogeneities across different data sources. We identified two key gaps and challenges in existing SDI studies that (1) many of the existing SDI studies used data from only single-level data sources (e.g., integrating individual-level patient records from different hospital systems), and (2) documentation of the data integration processes is sparse, threatening the reproducibility of SDI studies.
Collapse
Affiliation(s)
- Hansi Zhang
- Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Tianchen Lyu
- Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Pengfei Yin
- Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Sarah Bost
- Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Xing He
- Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Yi Guo
- Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Mattia Prosperi
- Department of Epidemiology, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Willian R Hogan
- Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Jiang Bian
- Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States.
| |
Collapse
|
4
|
Hannigan LJ, Phillippo DM, Hanlon P, Moss L, Butterly EW, Hawkins N, Dias S, Welton NJ, McAllister DA. Improving the Estimation of Subgroup Effects for Clinical Trial Participants with Multimorbidity by Incorporating Drug Class-Level Information in Bayesian Hierarchical Models: A Simulation Study. Med Decis Making 2021; 42:228-240. [PMID: 34407672 PMCID: PMC8777306 DOI: 10.1177/0272989x211029556] [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] [Indexed: 11/15/2022]
Abstract
Background There is limited guidance for using common drug therapies in the context of
multimorbidity. In part, this is because their effectiveness for patients
with specific comorbidities cannot easily be established using subgroup
analyses in clinical trials. Here, we use simulations to explore the
feasibility and implications of concurrently estimating effects of related
drug treatments in patients with multimorbidity by partially pooling
subgroup efficacy estimates across trials. Methods We performed simulations based on the characteristics of 161 real clinical
trials of noninsulin glucose-lowering drugs for diabetes, estimating
subgroup effects for patients with a hypothetical comorbidity across related
trials in different scenarios using Bayesian hierarchical generalized linear
models. We structured models according to an established ontology—the World
Health Organization Anatomic Chemical Therapeutic Classifications—allowing
us to nest all trials within drugs and all drugs within anatomic chemical
therapeutic classes, with effects partially pooled at each level of the
hierarchy. In a range of scenarios, we compared the performance of this
model to random effects meta-analyses of all drugs individually. Results Hierarchical, ontology-based Bayesian models were unbiased and accurately
recovered simulated comorbidity-drug interactions. Compared with single-drug
meta-analyses, they offered a relative increase in precision of up to 250%
in some scenarios because of information sharing across the hierarchy.
Because of the relative precision of the approaches, a large proportion of
small subgroup effects was detectable only using the hierarchical model. Conclusions By assuming that similar drugs may have similar subgroup effects, Bayesian
hierarchical models based on structures defined by existing ontologies can
be used to improve the precision of treatment efficacy estimates in patients
with multimorbidity, with potential implications for clinical decision
making.
Collapse
Affiliation(s)
- Laurie J Hannigan
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - David M Phillippo
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Peter Hanlon
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Laura Moss
- NHS Greater Glasgow & Clyde, UK.,School of Medicine, University of Glasgow, Glasgow, UK
| | - Elaine W Butterly
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Neil Hawkins
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Sofia Dias
- Centre for Reviews and Dissemination, University of York, York, North Yorkshire, UK
| | - Nicky J Welton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | |
Collapse
|
5
|
Chu J, Chen J, Chen X, Dong W, Shi J, Huang Z. Knowledge-aware multi-center clinical dataset adaptation: Problem, method, and application. J Biomed Inform 2021; 115:103710. [PMID: 33581323 DOI: 10.1016/j.jbi.2021.103710] [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: 09/23/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 11/30/2022]
Abstract
Adaptable utilization of clinical data collected from multiple centers, prompted by the need to overcome the shifts between the dataset distributions, and exploit these different datasets for potential clinical applications, has received significant attention in recent years. In this study, we propose a novel approach to this task by infusing an external knowledge graph (KG) into multi-center clinical data mining. Specifically, we propose an adversarial learning model to capture shared patient feature representations from multi-center heterogeneous clinical datasets, and employ an external KG to enrich the semantics of the patient sample by providing both clinical center-specific and center-general knowledge features, which are trained with a graph convolutional autoencoder. We evaluate the proposed model on a real clinical dataset extracted from the general cardiology wards of a Chinese hospital and a well-known public clinical dataset (MIMIC III, pertaining to ICU clinical settings) for the task of predicting acute kidney injury in patients with heart failure. The achieved experimental results demonstrate the efficacy of our proposed model.
Collapse
Affiliation(s)
- Jiebin Chu
- College of Biomedical Engineering and Instrument Science, Zhejiang University, China
| | - Jinbiao Chen
- College of Biomedical Engineering and Instrument Science, Zhejiang University, China
| | - Xiaofang Chen
- College of Biomedical Engineering and Instrument Science, Zhejiang University, China
| | - Wei Dong
- Department of Cardiology, Chinese PLA General Hospital, China
| | - Jinlong Shi
- Department of Medical Innovation Research, Medical Big Data Center, Chinese PLA General Hospital, China
| | - Zhengxing Huang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, China.
| |
Collapse
|
6
|
Zhang H, Guo Y, Prosperi M, Bian J. An ontology-based documentation of data discovery and integration process in cancer outcomes research. BMC Med Inform Decis Mak 2020; 20:292. [PMID: 33317497 PMCID: PMC7734720 DOI: 10.1186/s12911-020-01270-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 01/24/2023] Open
Abstract
Background To reduce cancer mortality and improve cancer outcomes, it is critical to understand the various cancer risk factors (RFs) across different domains (e.g., genetic, environmental, and behavioral risk factors) and levels (e.g., individual, interpersonal, and community levels). However, prior research on RFs of cancer outcomes, has primarily focused on individual level RFs due to the lack of integrated datasets that contain multi-level, multi-domain RFs. Further, the lack of a consensus and proper guidance on systematically identify RFs also increase the difficulty of RF selection from heterogenous data sources in a multi-level integrative data analysis (mIDA) study. More importantly, as mIDA studies require integrating heterogenous data sources, the data integration processes in the limited number of existing mIDA studies are inconsistently performed and poorly documented, and thus threatening transparency and reproducibility. Methods Informed by the National Institute on Minority Health and Health Disparities (NIMHD) research framework, we (1) reviewed existing reporting guidelines from the Enhancing the QUAlity and Transparency Of health Research (EQUATOR) network and (2) developed a theory-driven reporting guideline to guide the RF variable selection, data source selection, and data integration process. Then, we developed an ontology to standardize the documentation of the RF selection and data integration process in mIDA studies. Results We summarized the review results and created a reporting guideline—ATTEST—for reporting the variable selection and data source selection and integration process. We provided an ATTEST check list to help researchers to annotate and clearly document each step of their mIDA studies to ensure the transparency and reproducibility. We used the ATTEST to report two mIDA case studies and further transformed annotation results into sematic triples, so that the relationships among variables, data sources and integration processes are explicitly standardized and modeled using the classes and properties from OD-ATTEST. Conclusion Our ontology-based reporting guideline solves some key challenges in current mIDA studies for cancer outcomes research, through providing (1) a theory-driven guidance for multi-level and multi-domain RF variable and data source selection; and (2) a standardized documentation of the data selection and integration processes powered by an ontology, thus a way to enable sharing of mIDA study reports among researchers.
Collapse
Affiliation(s)
- Hansi Zhang
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, 2197 Mowry Road, Suite 122, PO Box 100177, Gainesville, FL, 32610-0177, USA
| | - Yi Guo
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, 2197 Mowry Road, Suite 122, PO Box 100177, Gainesville, FL, 32610-0177, USA.,Cancer Informatics & eHealth Core, University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Mattia Prosperi
- Department of Epidemiology, College of Medicine & College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, 2197 Mowry Road, Suite 122, PO Box 100177, Gainesville, FL, 32610-0177, USA. .,Cancer Informatics & eHealth Core, University of Florida Health Cancer Center, Gainesville, FL, USA.
| |
Collapse
|
7
|
Kondylakis H, Bucur A, Crico C, Dong F, Graf N, Hoffman S, Koumakis L, Manenti A, Marias K, Mazzocco K, Pravettoni G, Renzi C, Schera F, Triberti S, Tsiknakis M, Kiefer S. Patient empowerment for cancer patients through a novel ICT infrastructure. J Biomed Inform 2019; 101:103342. [PMID: 31816400 DOI: 10.1016/j.jbi.2019.103342] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022]
Abstract
As a result of recent advances in cancer research and "precision medicine" approaches, i.e. the idea of treating each patient with the right drug at the right time, more and more cancer patients are being cured, or might have to cope with a life with cancer. For many people, cancer survival today means living with a complex and chronic condition. Surviving and living with or beyond cancer requires the long-term management of the disease, leading to a significant need for active rehabilitation of the patients. In this paper, we present a novel methodology employed in the iManageCancer project for cancer patient empowerment in which personal health systems, serious games, psychoemotional monitoring and other novel decision-support tools are combined into an integrated patient empowerment platform. We present in detail the ICT infrastructure developed and our evaluation with the involvement of cancer patients on two sites, a large-scale pilot for adults and a small-scale test for children. The evaluation showed mixed evidences on the improvement of patient empowerment, while ability to cope with cancer, including improvement in mood and resilience to cancer, increased for the participants of the adults' pilot.
Collapse
Affiliation(s)
| | - Anca Bucur
- PHILIPS Research Europe, Eindhoven, The Netherlands
| | | | - Feng Dong
- Department of Computer Science and Technology, University of Bedfordshire, Luton, UK
| | - Norbert Graf
- Saarland University, Pediatric Oncology and Hematology, Homburg, Germany
| | | | | | | | - Kostas Marias
- Computational BioMedicine Laboratory, FORTH-ICS, Heraklion, Greece
| | | | | | | | - Fatima Schera
- Fraunhofer Institute for Biomedical Engineering, Germany
| | | | | | - Stephan Kiefer
- Fraunhofer Institute for Biomedical Engineering, Germany
| |
Collapse
|
8
|
Barrios CH, Reinert T, Werutsky G. Global Breast Cancer Research: Moving Forward. Am Soc Clin Oncol Educ Book 2018; 38:441-450. [PMID: 30231347 DOI: 10.1200/edbk_209183] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Breast cancer is a major global health problem and major cause of mortality. Although mortality trends are declining in high-income countries, trends are increasing in low- and middle-income countries (LMICs). Addressing global breast cancer research is a challenging endeavor, as notable disparities and extremely heterogeneous realities exist in different regions across the world. Basic global cancer health care needs have been addressed by the World Health Organization's (WHO) proposed list of essential medicines and by resource-stratified guidelines for screening and treatment. However, specific strategies are needed to address disparities in access to health care, particularly access to new therapies. Discussions about global research in breast cancer should take into account the ongoing globalization of clinical trials. Collaboration fostered by well-established research organizations in North America and Europe is essential for the development of infrastructure and human resources in LMICs so that researchers in these countries can begin to address regional questions. Specific challenges that impact the future of global breast cancer research include increasing the availability of trials in LMICs, developing strategies to increase patient participation in clinical trials, and creation of clear guidelines for the development of real-world evidence-based research. The main objective of this review is to encourage the discussion of challenges in global breast cancer research with the hope that collectively we will be able to generate workable proposals to advance the field.
Collapse
Affiliation(s)
- Carlos H Barrios
- From the Latin American Cooperative Oncology Group, Porto Alegre, Brazil
| | - Tomás Reinert
- From the Latin American Cooperative Oncology Group, Porto Alegre, Brazil
| | - Gustavo Werutsky
- From the Latin American Cooperative Oncology Group, Porto Alegre, Brazil
| |
Collapse
|
9
|
Maggi N, Gazzarata R, Ruggiero C, Lombardo C, Giacomini M. Cancer precision medicine today: Towards omic information in healthcare systems. TUMORI JOURNAL 2018; 105:38-46. [PMID: 30117369 DOI: 10.1177/0300891618792473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION: This article focuses on the integration of omics data in electronic health records and on interoperability aspects relating to big data analysis for precision medicine. METHODS: Omics data integration methods for electronic health record and for systems interoperability are considered, with special reference to the high number of specific software tools used to manage different aspects of patient treatment. This is an important barrier against the use of this integrated approach in daily clinical routine. RESULTS: The correct use of all three levels of interoperability (technical, semantic, and process interoperability) plays a key role in order to achieve an easy access to a significant amount of data, all with correct contextualization, which is the only way to obtain a real value from data for precision medicine. CONCLUSIONS: The proposed architecture could improve the potentialities of data routinely collected in many health information systems to form a real patient center information environment.
Collapse
Affiliation(s)
- Norbert Maggi
- 1 Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
| | | | - Carmelina Ruggiero
- 1 Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genova, Genova, Italy.,2 Healthropy s.r.l., Savona, Italy
| | - Claudio Lombardo
- 3 Sos Europe s.r.l., Genova, Italy.,4 Organisation of European Cancer Institutes-European Economic Interest Grouping, Brussels, Belgium
| | - Mauro Giacomini
- 1 Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genova, Genova, Italy.,2 Healthropy s.r.l., Savona, Italy.,5 Centre of Excellence for the study of molecular mechanisms involved in cell-to-cell communication: from basic research to the clinic (CEBR), Genova, Italy
| |
Collapse
|
10
|
The Vision of Personally Managed Health Data: Barriers, Approaches and Roadmap for the Future. J Biomed Inform 2018. [DOI: 10.1016/j.jbi.2018.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
11
|
Kasztelnik M, Coto E, Bubak M, Malawski M, Nowakowski P, Arenas J, Saglimbeni A, Testi D, Frangi AF. Support for Taverna workflows in the VPH-Share cloud platform. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2017; 146:37-46. [PMID: 28688488 DOI: 10.1016/j.cmpb.2017.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/27/2017] [Accepted: 05/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND OBJECTIVE To address the increasing need for collaborative endeavours within the Virtual Physiological Human (VPH) community, the VPH-Share collaborative cloud platform allows researchers to expose and share sequences of complex biomedical processing tasks in the form of computational workflows. The Taverna Workflow System is a very popular tool for orchestrating complex biomedical & bioinformatics processing tasks in the VPH community. This paper describes the VPH-Share components that support the building and execution of Taverna workflows, and explains how they interact with other VPH-Share components to improve the capabilities of the VPH-Share platform. METHODS Taverna workflow support is delivered by the Atmosphere cloud management platform and the VPH-Share Taverna plugin. These components are explained in detail, along with the two main procedures that were developed to enable this seamless integration: workflow composition and execution. RESULTS 1) Seamless integration of VPH-Share with other components and systems. 2) Extended range of different tools for workflows. 3) Successful integration of scientific workflows from other VPH projects. 4) Execution speed improvement for medical applications. CONCLUSION The presented workflow integration provides VPH-Share users with a wide range of different possibilities to compose and execute workflows, such as desktop or online composition, online batch execution, multithreading, remote execution, etc. The specific advantages of each supported tool are presented, as are the roles of Atmosphere and the VPH-Share plugin within the VPH-Share project. The combination of the VPH-Share plugin and Atmosphere engenders the VPH-Share infrastructure with far more flexible, powerful and usable capabilities for the VPH-Share community. As both components can continue to evolve and improve independently, we acknowledge that further improvements are still to be developed and will be described.
Collapse
Affiliation(s)
| | - Ernesto Coto
- Centre for Computational Imaging & Simulation Technologies in Biomedicine (CISTIB), Electronic and Electrical Engineering Department, The University of Sheffield, Sheffield, UK.
| | - Marian Bubak
- ACC Cyfronet AGH, Krakow, Poland; Department of Computer Science, AGH University of Science and Technology, Krakow, Poland.
| | - Maciej Malawski
- ACC Cyfronet AGH, Krakow, Poland; Department of Computer Science, AGH University of Science and Technology, Krakow, Poland.
| | | | - Juan Arenas
- Centre for Computational Imaging & Simulation Technologies in Biomedicine (CISTIB), Electronic and Electrical Engineering Department, The University of Sheffield, Sheffield, UK.
| | | | - Debora Testi
- CINECA SuperComputing Centre, Casalecchio di Reno, Italy.
| | - Alejandro F Frangi
- Centre for Computational Imaging & Simulation Technologies in Biomedicine (CISTIB), Electronic and Electrical Engineering Department, The University of Sheffield, Sheffield, UK.
| |
Collapse
|
12
|
Kondylakis H, Koumakis L, Hänold S, Nwankwo I, Forgó N, Marias K, Tsiknakis M, Graf N. Donor's support tool: Enabling informed secondary use of patient's biomaterial and personal data. Int J Med Inform 2016; 97:282-292. [PMID: 27919386 DOI: 10.1016/j.ijmedinf.2016.10.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/21/2016] [Accepted: 10/29/2016] [Indexed: 11/20/2022]
Abstract
PURPOSE Biomedical research is being catalyzed by the vast amount of data rapidly collected through the application of information technologies (IT). Despite IT advances, the methods for involving patients and citizens in biomedical research remain static, paper-based and organized around national boundaries and anachronistic legal frameworks. The purpose of this paper is to study the current practices for obtaining consent for biobanking and the legal requirements for reusing the available biomaterial and data in EU and finally to present a novel tool to this direction enabling the secondary use of data and biomaterial. METHOD We review existing European legislation for secondary use of patient's biomaterial and data for research, identify types and scopes of consent, formal requirements for consent, and consider their implications for implementing electronic consent tools. To this direction, we proceed further to develop a modular tool, named Donor's Support Tool (DST), designed to connect researchers with participants, and to promote engagement, informed participation and individual decision making. RESULTS To identify the advantages of our solution we compare our tool with six other relevant approaches. The results show that our tool scores higher than the other tools in functionality, security and intelligence whereas it is the only one free and open-source. In addition, the potential of our solution is shown by a proof of concept deployment in an existing clinical setting, where it was really appreciated, as streamlining the relevant workflow.
Collapse
Affiliation(s)
- Haridimos Kondylakis
- Computational BioMedicine Laboratory, FORTH-ICS, N. Plastira 100, Heraklion, Greece.
| | - Lefteris Koumakis
- Computational BioMedicine Laboratory, FORTH-ICS, N. Plastira 100, Heraklion, Greece
| | - Stephanie Hänold
- Institute for Legal Informatics, Leibniz Universität Hannover, Königsworther Platz 1, 30167 Hannover, Germany
| | - Iheanyi Nwankwo
- Institute for Legal Informatics, Leibniz Universität Hannover, Königsworther Platz 1, 30167 Hannover, Germany
| | - Nikolaus Forgó
- Institute for Legal Informatics, Leibniz Universität Hannover, Königsworther Platz 1, 30167 Hannover, Germany
| | - Kostas Marias
- Computational BioMedicine Laboratory, FORTH-ICS, N. Plastira 100, Heraklion, Greece
| | - Manolis Tsiknakis
- Computational BioMedicine Laboratory, FORTH-ICS, N. Plastira 100, Heraklion, Greece; Department of Informatics Engineering, Technological Educational Institute of Crete, Estavromenos 71004, Heraklion, Crete, Greece
| | - Norbert Graf
- Department for Pediatric Oncology and Hematology, Saarland University Hospital, Homburg, Germany
| |
Collapse
|