1) Norway has established an archetype governance model to develop shared clinical information models using openEHR in order to achieve semantic interoperability across its healthcare system.
2) The governance model involves national editorial committees, regional representatives, and clinicians collaborating online using specific tools to develop, review, and approve archetypes according to a formalized process.
3) Over 60 archetypes have been published so far covering basic clinical concepts like observations, diagnoses, and medications, though engagement of certain specialties remains a challenge.
Standards in health informatics - problem, clinical models and terminologySilje Ljosland Bakke
- Clinical information must be structured using shared and standardized clinical models and terminologies to enable semantic interoperability, longitudinal record access, and clinical decision support. However, structuring health information is complex due to the diversity and dynamic nature of clinical data.
- openEHR provides a free and open specification for structured health records, separating the reference model from archetypes and templates to define clinical content in a reusable way. National governance is needed to develop, review, and publish archetypes.
- Information models and terminologies are complementary - models define data structure while terminologies provide controlled vocabularies, but neither is sufficient alone due to contextual needs and complex concepts. Pragmatic choices must be made based on use case
This document discusses Norway's national governance of clinical archetypes. It provides an overview of Norway's public hospital system and use of openEHR archetypes. A national archetype governance scheme was established in 2013 by National ICT Norway to develop high quality archetypes through a review and approval process. The scheme aims for semantic interoperability through shared archetypes. Key success factors include clinician involvement, appropriate tools, dedicated resources, and international collaboration. While progress has been made approving archetypes, continued challenges include translation efforts and aligning archetype development with review timelines.
Workshop on educating the workshop for openEHR implementation at Medinfo 2015Silje Ljosland Bakke
This document discusses strategies for educating healthcare professionals on openEHR implementation at a national level. It recommends having:
1) A governance model and rules with sponsor support for tools, time, and training.
2) Buy-in from decision makers by explaining the economic and interoperability benefits of a unified information modeling approach.
3) Clinician engagement by recognizing their interests and expertise, and explaining how openEHR can help achieve their goals in areas like quality improvement.
4) Training programs at different levels and for various roles defined for the openEHR implementation.
This document discusses the differences and relationships between terminologies and information models. Terminologies provide controlled vocabularies and classifications that can be used to provide answers, while information models define questions and structure for complex concepts. Terminologies are useful for diagnoses, procedures, medications and other concepts that exist in reality, while information models are better for defining context and quantitative data. Both have roles to play but also have limitations, so pragmatic choices are needed regarding their use.
Enabling Clinical Data Reuse with openEHR Data Warehouse EnvironmentsLuis Marco Ruiz
Modern medicine needs methods to enable access to data,
captured during health care, for research, surveillance,
decision support and other reuse purposes. Initiatives like the
National Patient Centered Clinical Research Network in the
US and the Electronic Health Records for Clinical Research
in the EU are facilitating the reuse of Electronic Health
Record (EHR) data for clinical research. One of the barriers
for data reuse is the integration and interoperability of
different Healthcare Information Systems (HIS). The reason is
the differences among the HIS information and terminology
models. The use of EHR standards like openEHR can alleviate
these barriers providing a standard, unambiguous,
semantically enriched representation of clinical data to
enable semantic interoperability and data integration. Few
works have been published describing how to drive
proprietary data stored in EHRs into standard openEHR
repositories. This tutorial provides an overview of the key
concepts, tools and techniques necessary to implement an
openEHR-based Data Warehouse (DW) environment to reuse
clinical data. We aim to provide insights into data extraction
from proprietary sources, transformation into openEHR
compliant instances to populate a standard repository and
enable access to it using standard query languages and
services
Henning Müller et Michael Schumacher pour la journée e-health 2013Thearkvalais
The document summarizes the work of the eHealth unit at HES-SO in Sierre, Switzerland. It conducts applied research in eHealth with the goal of supporting the health domain by connecting data and interpreting multiple sources for reliable decision making. Some of its projects include developing tools for monitoring and managing gestational diabetes, extracting concepts from medical images for similar case retrieval, and creating an infrastructure to integrate complex patient data from multiple sources to simulate treatment outcomes.
A l'occasion de la première journée eHealth du 7 juin 2013, Prof. Henning Müller et Prof. Michael Schumacher ont présenté les projets de recherche eHealth de notre institut.
1) Norway has established an archetype governance model to develop shared clinical information models using openEHR in order to achieve semantic interoperability across its healthcare system.
2) The governance model involves national editorial committees, regional representatives, and clinicians collaborating online using specific tools to develop, review, and approve archetypes according to a formalized process.
3) Over 60 archetypes have been published so far covering basic clinical concepts like observations, diagnoses, and medications, though engagement of certain specialties remains a challenge.
Standards in health informatics - problem, clinical models and terminologySilje Ljosland Bakke
- Clinical information must be structured using shared and standardized clinical models and terminologies to enable semantic interoperability, longitudinal record access, and clinical decision support. However, structuring health information is complex due to the diversity and dynamic nature of clinical data.
- openEHR provides a free and open specification for structured health records, separating the reference model from archetypes and templates to define clinical content in a reusable way. National governance is needed to develop, review, and publish archetypes.
- Information models and terminologies are complementary - models define data structure while terminologies provide controlled vocabularies, but neither is sufficient alone due to contextual needs and complex concepts. Pragmatic choices must be made based on use case
This document discusses Norway's national governance of clinical archetypes. It provides an overview of Norway's public hospital system and use of openEHR archetypes. A national archetype governance scheme was established in 2013 by National ICT Norway to develop high quality archetypes through a review and approval process. The scheme aims for semantic interoperability through shared archetypes. Key success factors include clinician involvement, appropriate tools, dedicated resources, and international collaboration. While progress has been made approving archetypes, continued challenges include translation efforts and aligning archetype development with review timelines.
Workshop on educating the workshop for openEHR implementation at Medinfo 2015Silje Ljosland Bakke
This document discusses strategies for educating healthcare professionals on openEHR implementation at a national level. It recommends having:
1) A governance model and rules with sponsor support for tools, time, and training.
2) Buy-in from decision makers by explaining the economic and interoperability benefits of a unified information modeling approach.
3) Clinician engagement by recognizing their interests and expertise, and explaining how openEHR can help achieve their goals in areas like quality improvement.
4) Training programs at different levels and for various roles defined for the openEHR implementation.
This document discusses the differences and relationships between terminologies and information models. Terminologies provide controlled vocabularies and classifications that can be used to provide answers, while information models define questions and structure for complex concepts. Terminologies are useful for diagnoses, procedures, medications and other concepts that exist in reality, while information models are better for defining context and quantitative data. Both have roles to play but also have limitations, so pragmatic choices are needed regarding their use.
Enabling Clinical Data Reuse with openEHR Data Warehouse EnvironmentsLuis Marco Ruiz
Modern medicine needs methods to enable access to data,
captured during health care, for research, surveillance,
decision support and other reuse purposes. Initiatives like the
National Patient Centered Clinical Research Network in the
US and the Electronic Health Records for Clinical Research
in the EU are facilitating the reuse of Electronic Health
Record (EHR) data for clinical research. One of the barriers
for data reuse is the integration and interoperability of
different Healthcare Information Systems (HIS). The reason is
the differences among the HIS information and terminology
models. The use of EHR standards like openEHR can alleviate
these barriers providing a standard, unambiguous,
semantically enriched representation of clinical data to
enable semantic interoperability and data integration. Few
works have been published describing how to drive
proprietary data stored in EHRs into standard openEHR
repositories. This tutorial provides an overview of the key
concepts, tools and techniques necessary to implement an
openEHR-based Data Warehouse (DW) environment to reuse
clinical data. We aim to provide insights into data extraction
from proprietary sources, transformation into openEHR
compliant instances to populate a standard repository and
enable access to it using standard query languages and
services
Henning Müller et Michael Schumacher pour la journée e-health 2013Thearkvalais
The document summarizes the work of the eHealth unit at HES-SO in Sierre, Switzerland. It conducts applied research in eHealth with the goal of supporting the health domain by connecting data and interpreting multiple sources for reliable decision making. Some of its projects include developing tools for monitoring and managing gestational diabetes, extracting concepts from medical images for similar case retrieval, and creating an infrastructure to integrate complex patient data from multiple sources to simulate treatment outcomes.
A l'occasion de la première journée eHealth du 7 juin 2013, Prof. Henning Müller et Prof. Michael Schumacher ont présenté les projets de recherche eHealth de notre institut.
Researchers and care providers wanted to have access to all of the patients` vitals signs (temperature, blood pressure, heart rate, and respiratory rate) but most of this data wasn?t recorded, only a few readings a day were posted to the patients Electronic Medical Record (EMR). The EMR isn`t meant to store such volume of data, let alone to perform any data mining on it. This session will describe the architecture of the solution that was implemented to collect these vital signs automatically from Bedside Medical Devices (BDMI), and store them into a temporary storage, then load them into a Hadoop cluster. The session will also cover how the team married this vital signs data in the HDFS (Hadoop File System) with the rest of the EMR data for our Principles Investigators (PI) in our research institute to search for correlations between administered medications, diagnosis, and vital signs readings. The session will describe the reasons behind the design decisions that were made, such as using a Cloud Hadoop cluster versus on-premises while maintaining HIPAA.
This document discusses medical data and its importance. It defines key terms like data, information and knowledge. It explains how medical data is collected and used by various stakeholders in healthcare. It also outlines the peculiarities of medical data and challenges with traditional record keeping. Finally, it discusses important data sources, users, and agencies involved in medical data in India.
Personalized Medicine with IBM-Watson: Future of Cancer carejetweedy
Watson for Genomics uses IBM's Watson cognitive computing system to help personalize cancer care. It analyzes genomic sequencing data and clinical records to provide treatment suggestions and clinical trial matches for patients in minutes, compared to weeks for traditional approaches. Researchers are finalizing the algorithm and testing it in clinical trials. Watson draws from a large corpus of medical literature and patient data to understand questions, generate hypotheses, and provide evidence to support its answers. It could help reduce health professionals' workload and improve access to care, though challenges remain in developing the algorithm and acquiring sufficient data sets.
openEHR Approach to Detailed Clinical Models (DCM) Development - Lessons Lear...Koray Atalag
Presented at Health Informatics New Zealand (HINZ 2017) Conference, 1-3 Nov 2017, Rotorua, New Zealand. Based on my Masters student Peter Wei's research. Authorship: Ping-Cheng Wei, Koray Atalag and Karen Day from the University of Auckland.
RDAP 16 Poster: Measuring adoption of Electronic Lab Notebooks and their impa...ASIS&T
This document discusses challenges in measuring adoption and impact of electronic lab notebooks (ELNs) for research data management. It provides background on ELN implementation at Cornell and Wisconsin universities and describes prior efforts to survey ELN users about data management practices. Specifically, it examines difficulties in defining and assessing concepts like data management and adoption, and getting user perspectives on the value of ELNs for record keeping, metadata capture, and archiving data over time. Input is sought on how to improve questions that evaluate the degree to which ELNs help with various data management needs and goals.
RDAP 16 Poster: Responding to Data Management and Sharing Requirements in the...ASIS&T
Research Data Access and Preservation Summit, 2016
Atlanta, GA
May 4-7, 2016
Poster session (Wednesday, May 4)
Presenter:
Caitlin Bakker, University of Minnesota
UCSF Informatics Day 2014 - Ida Sim, "Informatics Technologies: From a Data-C...CTSI at UCSF
This document discusses moving from a data-centric to a hypothesis-centric view of clinical and translational research using electronic health records and other informatics technologies. It notes that most current research is observational rather than interventional, and outlines ways informatics could better support hypothesis testing through virtual, community-based, and point-of-care clinical trials by integrating risk calculators, structured note templates, surveys, and other tools directly into clinical workflows and patient portals. The presentation calls for further developing these informatics capabilities to facilitate more interventional research at lower cost.
Interoperability Between Healthcare ApplicationsJohn Gillson
The document discusses interoperability between heterogeneous healthcare information systems. It describes standards for achieving interoperability, including HL7 versions 2 and 3 for message exchange, the Reference Information Model (RIM), Clinical Document Architecture (CDA), and Integrating the Healthcare Enterprise (IHE) profiles like Cross-Enterprise Document Sharing (XDS). It also discusses electronic health records (EHRs), master patient indexes (MPIs), virtual medical records (VMRs), and how the Professional Exchange Server (PXS) can bridge gaps between disparate healthcare systems through its various components.
This document discusses developing a FHIR-based API for OpenMRS to improve interoperability. It covers the need for interoperability in healthcare and limitations of current standards like HL7 V2. FHIR is presented as a promising new standard that addresses many issues. The document outlines plans to build basic FHIR import/export capabilities in OpenMRS to allow resource exchange and integration with platforms like SMART. The goal is to explore how far a FHIR-based approach can go in supporting interoperability and establishing FHIR as a core OpenMRS standard.
Presentation by Hugo Leroux and Liming Zhu, CSIRO, to the 'Unlocking value from publicly funded Clinical Research Data' workshop, cohosted by ARDC and CSIRO at ANU on 6 March 2019.
A Comparison of Non-Dictionary Based Approaches to Automate Cancer Detection Using Plaintext Medical Data with Dr. Shaun Grannis, Dr. Brian Dixon et. al. presented at the Regenstrief WIP (7th Jan 2015)
In this full-day tutorial, you will learn basic overview of electronic medical records systems, health data management and how you can use the OpenMRS system for data and information management. We will cover basics of installation, user management, location management, patient dashboards and some interesting features that are provided by different modules. You can see how OpenMRS can be customized with different modules that are suitable for different contexts. This tutorial is helpful for new users and developers who would like to know the features of OpenMRS. Individuals who would like to evaluate and try to see if OpenMRS fits their healthcare needs will also benefit from this tutorial.
Data Preparation and Visualization for Monitoring NCDs MortalityRamon Martinez
This is the slide deck of my talk at the Alteryx webinar Tableau Zen Masters - Preparing Data for the Conference, Oct 13, 2015.
It describes how we prepare data for analysis and visualization, particularly for assessing the trends of premature mortality from noncommunicable diseases.
Applications of analytics and visualizations in PAHORamon Martinez
This presentation introduces current practices for data analysis and visualizations in the Pan American Health Organization (PAHO).
The PAHO Health Information and Intelligence Platform is presented as key resource to facilitate data access and use, generation of information and insights, and dissemination of information internally and to the general public. Some use cases were illustrated highlighting how PAHO has benefited from the application of visual analytics.
Is that a scientific report or just some cool pictures from the lab? Reproduc...Greg Landrum
Requirements for reproducibility in computational chemistry publications include making available the data, code or algorithms, and results from the study. Authors should provide all data necessary to understand and assess their conclusions. Source code or detailed algorithm descriptions should also be included to allow independent reproduction of the work. Finally, publications must contain the actual results from applying the method rather than just describing results. Adopting these standards of transparency helps ensure others can evaluate and build upon published research claims.
Oxford DTP - Sansone - Data publications and Scientific Data - Dec 2014Susanna-Assunta Sansone
- The document discusses the need for open and accessible data in research. It notes that over 50% of studies are not published due to selective reporting of results.
- There is a movement for "FAIR data" in life and medical sciences, where data is findable, accessible, interoperable, and reusable. However, not much data currently meets these standards.
- Publishers can play a role in incentivizing data sharing by implementing policies requiring data availability and format standards for publishing research. This includes supporting data citations and data journals.
This document provides an overview of data analytics topics including big data, database structure and management, and statistical analysis. It introduces big data concepts like volume, velocity, variety and veracity. It discusses database structure, relationships, and how to manage data through roadmaps and health checks. It also introduces statistical concepts like descriptive statistics, distributions, and regression analysis and how they can be applied in healthcare.
Presentation on Evaluating Methods for the Identification of Cancer in Free-Text Pathology Reports Using alternative Machine Learning and Data Preprocessing Approaches
Tools to Drive Enrollment OCT Arena-Boston-2015Dan Diaz
The 4th Annual Clinical Operations in Oncology Trials East Coast was an amazing hit. Over 25 speakers challenged the 200 attendees on how- "WE" as an industry can use new tools and strategies to better our Clinical Trial Execution and Patient Enrollment.
With only 3% of the patients in the USA participating in Cancer Trials- we have to do a better job finding ways to educate them about the benefits of clinical studies.
The following tools are some of the new enhancements for better site and physician selection which can help find better results.
Machine learning, health data & the limits of knowledgePaul Agapow
Lecture for Imperial College London's MSc in Health Data Analytics, critiquing a recent paper on COVID diagnosis and moving out to talk about good practices (& limits) in ML and model building
Researchers and care providers wanted to have access to all of the patients` vitals signs (temperature, blood pressure, heart rate, and respiratory rate) but most of this data wasn?t recorded, only a few readings a day were posted to the patients Electronic Medical Record (EMR). The EMR isn`t meant to store such volume of data, let alone to perform any data mining on it. This session will describe the architecture of the solution that was implemented to collect these vital signs automatically from Bedside Medical Devices (BDMI), and store them into a temporary storage, then load them into a Hadoop cluster. The session will also cover how the team married this vital signs data in the HDFS (Hadoop File System) with the rest of the EMR data for our Principles Investigators (PI) in our research institute to search for correlations between administered medications, diagnosis, and vital signs readings. The session will describe the reasons behind the design decisions that were made, such as using a Cloud Hadoop cluster versus on-premises while maintaining HIPAA.
This document discusses medical data and its importance. It defines key terms like data, information and knowledge. It explains how medical data is collected and used by various stakeholders in healthcare. It also outlines the peculiarities of medical data and challenges with traditional record keeping. Finally, it discusses important data sources, users, and agencies involved in medical data in India.
Personalized Medicine with IBM-Watson: Future of Cancer carejetweedy
Watson for Genomics uses IBM's Watson cognitive computing system to help personalize cancer care. It analyzes genomic sequencing data and clinical records to provide treatment suggestions and clinical trial matches for patients in minutes, compared to weeks for traditional approaches. Researchers are finalizing the algorithm and testing it in clinical trials. Watson draws from a large corpus of medical literature and patient data to understand questions, generate hypotheses, and provide evidence to support its answers. It could help reduce health professionals' workload and improve access to care, though challenges remain in developing the algorithm and acquiring sufficient data sets.
openEHR Approach to Detailed Clinical Models (DCM) Development - Lessons Lear...Koray Atalag
Presented at Health Informatics New Zealand (HINZ 2017) Conference, 1-3 Nov 2017, Rotorua, New Zealand. Based on my Masters student Peter Wei's research. Authorship: Ping-Cheng Wei, Koray Atalag and Karen Day from the University of Auckland.
RDAP 16 Poster: Measuring adoption of Electronic Lab Notebooks and their impa...ASIS&T
This document discusses challenges in measuring adoption and impact of electronic lab notebooks (ELNs) for research data management. It provides background on ELN implementation at Cornell and Wisconsin universities and describes prior efforts to survey ELN users about data management practices. Specifically, it examines difficulties in defining and assessing concepts like data management and adoption, and getting user perspectives on the value of ELNs for record keeping, metadata capture, and archiving data over time. Input is sought on how to improve questions that evaluate the degree to which ELNs help with various data management needs and goals.
RDAP 16 Poster: Responding to Data Management and Sharing Requirements in the...ASIS&T
Research Data Access and Preservation Summit, 2016
Atlanta, GA
May 4-7, 2016
Poster session (Wednesday, May 4)
Presenter:
Caitlin Bakker, University of Minnesota
UCSF Informatics Day 2014 - Ida Sim, "Informatics Technologies: From a Data-C...CTSI at UCSF
This document discusses moving from a data-centric to a hypothesis-centric view of clinical and translational research using electronic health records and other informatics technologies. It notes that most current research is observational rather than interventional, and outlines ways informatics could better support hypothesis testing through virtual, community-based, and point-of-care clinical trials by integrating risk calculators, structured note templates, surveys, and other tools directly into clinical workflows and patient portals. The presentation calls for further developing these informatics capabilities to facilitate more interventional research at lower cost.
Interoperability Between Healthcare ApplicationsJohn Gillson
The document discusses interoperability between heterogeneous healthcare information systems. It describes standards for achieving interoperability, including HL7 versions 2 and 3 for message exchange, the Reference Information Model (RIM), Clinical Document Architecture (CDA), and Integrating the Healthcare Enterprise (IHE) profiles like Cross-Enterprise Document Sharing (XDS). It also discusses electronic health records (EHRs), master patient indexes (MPIs), virtual medical records (VMRs), and how the Professional Exchange Server (PXS) can bridge gaps between disparate healthcare systems through its various components.
This document discusses developing a FHIR-based API for OpenMRS to improve interoperability. It covers the need for interoperability in healthcare and limitations of current standards like HL7 V2. FHIR is presented as a promising new standard that addresses many issues. The document outlines plans to build basic FHIR import/export capabilities in OpenMRS to allow resource exchange and integration with platforms like SMART. The goal is to explore how far a FHIR-based approach can go in supporting interoperability and establishing FHIR as a core OpenMRS standard.
Presentation by Hugo Leroux and Liming Zhu, CSIRO, to the 'Unlocking value from publicly funded Clinical Research Data' workshop, cohosted by ARDC and CSIRO at ANU on 6 March 2019.
A Comparison of Non-Dictionary Based Approaches to Automate Cancer Detection Using Plaintext Medical Data with Dr. Shaun Grannis, Dr. Brian Dixon et. al. presented at the Regenstrief WIP (7th Jan 2015)
In this full-day tutorial, you will learn basic overview of electronic medical records systems, health data management and how you can use the OpenMRS system for data and information management. We will cover basics of installation, user management, location management, patient dashboards and some interesting features that are provided by different modules. You can see how OpenMRS can be customized with different modules that are suitable for different contexts. This tutorial is helpful for new users and developers who would like to know the features of OpenMRS. Individuals who would like to evaluate and try to see if OpenMRS fits their healthcare needs will also benefit from this tutorial.
Data Preparation and Visualization for Monitoring NCDs MortalityRamon Martinez
This is the slide deck of my talk at the Alteryx webinar Tableau Zen Masters - Preparing Data for the Conference, Oct 13, 2015.
It describes how we prepare data for analysis and visualization, particularly for assessing the trends of premature mortality from noncommunicable diseases.
Applications of analytics and visualizations in PAHORamon Martinez
This presentation introduces current practices for data analysis and visualizations in the Pan American Health Organization (PAHO).
The PAHO Health Information and Intelligence Platform is presented as key resource to facilitate data access and use, generation of information and insights, and dissemination of information internally and to the general public. Some use cases were illustrated highlighting how PAHO has benefited from the application of visual analytics.
Is that a scientific report or just some cool pictures from the lab? Reproduc...Greg Landrum
Requirements for reproducibility in computational chemistry publications include making available the data, code or algorithms, and results from the study. Authors should provide all data necessary to understand and assess their conclusions. Source code or detailed algorithm descriptions should also be included to allow independent reproduction of the work. Finally, publications must contain the actual results from applying the method rather than just describing results. Adopting these standards of transparency helps ensure others can evaluate and build upon published research claims.
Oxford DTP - Sansone - Data publications and Scientific Data - Dec 2014Susanna-Assunta Sansone
- The document discusses the need for open and accessible data in research. It notes that over 50% of studies are not published due to selective reporting of results.
- There is a movement for "FAIR data" in life and medical sciences, where data is findable, accessible, interoperable, and reusable. However, not much data currently meets these standards.
- Publishers can play a role in incentivizing data sharing by implementing policies requiring data availability and format standards for publishing research. This includes supporting data citations and data journals.
This document provides an overview of data analytics topics including big data, database structure and management, and statistical analysis. It introduces big data concepts like volume, velocity, variety and veracity. It discusses database structure, relationships, and how to manage data through roadmaps and health checks. It also introduces statistical concepts like descriptive statistics, distributions, and regression analysis and how they can be applied in healthcare.
Presentation on Evaluating Methods for the Identification of Cancer in Free-Text Pathology Reports Using alternative Machine Learning and Data Preprocessing Approaches
Tools to Drive Enrollment OCT Arena-Boston-2015Dan Diaz
The 4th Annual Clinical Operations in Oncology Trials East Coast was an amazing hit. Over 25 speakers challenged the 200 attendees on how- "WE" as an industry can use new tools and strategies to better our Clinical Trial Execution and Patient Enrollment.
With only 3% of the patients in the USA participating in Cancer Trials- we have to do a better job finding ways to educate them about the benefits of clinical studies.
The following tools are some of the new enhancements for better site and physician selection which can help find better results.
Machine learning, health data & the limits of knowledgePaul Agapow
Lecture for Imperial College London's MSc in Health Data Analytics, critiquing a recent paper on COVID diagnosis and moving out to talk about good practices (& limits) in ML and model building
Data Harmonization for a Molecularly Driven Health SystemWarren Kibbe
Maximizing the value of data, computing, data science in an academic medical center, or 'towards a molecularly informed Learning Health System. Given in October at the University of Florida in Gainesville
This document discusses how Hadoop can enable healthcare by providing a modern data platform. Currently, electronic medical records and data warehouses have limitations in processing high volumes of real-time data and performing advanced analytics. A Hadoop-based big data platform can ingest all healthcare data in its native format and in real time. This allows for use cases like early detection of sepsis, predicting readmissions, and advanced research. The architecture is designed to be scalable, use open source tools, and store all healthcare data for advanced analytics to improve patient care and outcomes.
Sdal air health and social development (jan. 27, 2014) finalkimlyman
This document summarizes a workshop on health and social development analytics using big data. It discusses how data sources are becoming larger, more diverse and used for multiple purposes. This presents opportunities to better understand issues but also challenges around privacy, bias and data quality. The workshop aims to identify partnership opportunities and prototype projects using integrated data to address health and social issues. Case studies from various institutions are presented using combined data sources like medical records, surveys and environmental factors.
Semantic Web & Web 3.0 empowering real world outcomes in biomedical research ...Amit Sheth
Talk presented in Spain (WiMS 2013/UAM-Madrid, UMA-Malaga), June 2013.
Replaces earlier version at: http://www.slideshare.net/apsheth/semantic-technology-empowering-real-world-outcomes-in-biomedical-research-and-clinical-practices
Biomedical and translational research as well as clinical practice are increasingly data driven. Activities routinely involve large number of devices, data and people, resulting in the challenges associated with volume, velocity (change), variety (heterogeneity) and veracity (provenance, quality). Equally important is to realize the challenge of serving the needs of broader ecosystems of people and organizations, extending traditional stakeholders like drug makers, clinicians and policy makers, to increasingly technology savvy and information empowered patients. We believe that semantics is becoming centerpiece of informatics solutions that convert data into meaningful, contextually relevant information and insights that lead to optimal decisions for translational research and 360 degree health, fitness and well-being.
In this talk, I will provide a series of snapshots of efforts in which semantic approach and technology is the key enabler. I will emphasize real-world and in-use projects, technologies and systems, involving significant collaborations between my team and biomedical researchers or practicing clinicians. Examples include:
• Active Semantic Electronic Medical Record
• Semantics and Services enabled Problem Solving Environment for T.cruzi (SPSE)
• Data Mining of Cardiology data
• Semantic Search, Browsing and Literature Based Discovery
• PREscription Drug abuse Online Surveillance and Epidemiology (PREDOSE)
• kHealth: development of a knowledge-enhanced sensing and mobile computing applications (using low cost sensors and smartphone), along with ability to convert low level observations into clinically relevant abstractions
Further details are at http://knoesis.org/amit/hcls
Utility and Added Value of Classifications in Health Information SystemsBedirhan Ustun
Health Information Systems; ICD, ICD11, SNOMED-CT, Use Cases showing benefits of use of classification- terminology systems; avoid and e-tower of Babel; electronic health record, Enhance Patient Care, Decision Support, Safety & Quality
Data supporting precision oncology fda wakibbeWarren Kibbe
This document discusses how data is supporting precision oncology through three main points:
1) Our ability to generate and analyze biomedical data continues to grow in terms of variety and volume from sources like genomics and imaging.
2) Analyzing multi-scale, multi-modal temporal data requires advances in data science like machine learning and artificial intelligence.
3) Standards like FAIR data principles are needed to enable data sharing and the creation of a learning health system for cancer through harmonization and interoperability of data.
Clinical Research Informatics Year-in-Review 2024Peter Embi
Peter Embi, MD's presentation of Clinical Research Informatics year-in-review presented at the 2024 AMIA Informatics Summit in Boston, MA on March 20, 2024.
This paper describes the methods of the Treatment In Morning versus Evening (TIME) study, a large prospective randomized open-label blinded endpoint study comparing morning versus evening dosing of antihypertensive medications. The TIME study recruits participants through advertising, primary and secondary care, and patient databases in the UK. Participants self-enroll and consent on a secure website, and are randomized to morning or evening dosing. Follow-ups are conducted by automated email at 1 month and every 3 months thereafter. The study uses a prospective randomized open-label blinded endpoint design to establish if evening dosing is more cardioprotective than morning dosing.
A brief presentation outlining the concepts of data quality in the context of clinical data, and highlighting the importance of data quality for population health, health analytics, and other secondary uses of clinical data.
The Learning Health System: Thinking and Acting Across ScalesPhilip Payne
A Learning Health System (LHS) can be defined as an environment in which knowledge generation processes are embedded into daily clinical practice in order to continually improve the quality, safety, and outcomes of healthcare delivery. While still largely an aspirational goal, the promise of the LHS is a future in which every patient encounter is an opportunity to learn and improve that patient’s care, as well as the care their family and broader community receives. The foundation for building such an LHS can and should be the Electronic Health Record (EHR), which provides the basis for the comprehensive instrumentation and measurement of clinical phenotypes, as well as a means of delivering new evidence at the patient- and population levels. In this presentation, we will explore the ways in which such EHR-derived phenotypes can be combined with complementary data across a spectrum from biomolecules to population level trends, to both generate insights and deliver such knowledge in the right time, place, and format, ultimately improving clinical outcomes and value.
A VIVO VIEW OF CANCER RESEARCH: Dream, Vision and RealityPaul Courtney
Presentation made by Paul Courtney (Dana-Farber Cancer Institute, Boston, MA and OHSL, MD) and Anil Srivastava (OHSL) at the 2013 VIVO conference in St. Louis, MO. Material contributed by Rubayi Srivastava (OHSL), Swati Mehta (Centre for Development of Advanced Computing, India), Juliusz Pukacki (Poznan Supercomputing and Network Center, Poland) and Devdatt Dubhashi (Chalmers Institute of Technology, Sweden).
Will Biomedical Research Fundamentally Change in the Era of Big Data?Philip Bourne
This document discusses how biomedical research may fundamentally change in the era of big data. It notes that biomedical research has always been data-driven, but the scope, variety, complexity and volume of data is now much greater. It also discusses the need for more open data sharing and new tools and methods for large-scale analysis. The document suggests biomedical research may move towards a more collaborative "platform" model, as seen with companies like Airbnb, with the goal of improving data access, reuse and reproducibility of research. However, overcoming challenges like incentives, trust and work practices will be important for any new platform to succeed.
This document provides an overview of health informatics and the role of librarians. It defines key terms like electronic health records, health information technology, and meaningful use. It discusses stages of meaningful use and how health informatics tools can improve care delivery and outcomes. The document also explores potential roles for librarians in areas like patient education, training, and research support within the health informatics field.
Ontologies: What Librarians Need to KnowBarry Smith
Barry Smith presented on ontologies and what librarians need to know about them. Ontologies provide controlled vocabularies that can be used to tag and annotate data in order to integrate datasets and avoid data silos. The Gene Ontology is highlighted as a successful ontology due to factors such as being developed and maintained by domain experts according to best practices, having over 11 million annotations linking genes to ontology terms, and enabling new types of biological research through analysis and comparison of massive quantities of annotated data. For ontologies to fully realize their potential to remove data silos, they must be prospectively standardized and evolved based on user feedback.
The document discusses how AI and machine learning can help address challenges in healthcare by analyzing complex medical data. It provides examples of how AI can help with tasks like analyzing medical images to assist radiologists, predicting drug response from scans, and using electronic health records to better understand diseases and patient heterogeneity. The document also acknowledges challenges like the need for large labeled datasets and ensuring interpretability and avoidance of bias.
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The document summarizes the barriers to using clinical data from the UK National Health Service (NHS) for research purposes and potential solutions. It discusses issues with data quality, coding, and linking records across disconnected systems. However, integrated electronic health records could enable large cohort studies and clinical trials if privacy and security are ensured. The author proposes training for clinical and research staff on database design, standards, and information sharing to help align records and support strategic health research using NHS data.
OpenMRS is an open source medical record system platform and global community. It was created in 2004 to improve healthcare in resource-constrained environments by providing a robust and scalable electronic medical record system. OpenMRS is patient-centric, modular, and standards-based. It has been implemented around the world for various uses such as disease-specific records, inpatient care, research, and more. The OpenMRS community has learned that solutions should be user-centered, reuse existing materials when possible, and have a flexible foundation while following thoughts with action. OpenMRS is best suited for organizations wanting to capture longitudinal patient data to improve care over time.
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An introduction to openEHR, clinical information modelling, pragmatic standardisation and use of ontologies.
Presented by Erik Sundvall and Silje Ljosland Bakke in CRS4, Sardinia, on 11 october 2022, as part of InterHealth 2022.
Silje Ljosland Bakke gave a presentation on health information technology. She discussed why health data is not structured like banking data and asked what makes collecting and sharing health data between hospitals so difficult. Nightingale was quoted as saying that obtaining comparable hospital records in the 1860s would help answer many questions, but they were rarely available. Bakke thanked the audience for listening and noted that while structured data is important, it is not a perfect solution.
The document discusses Norway's approach to standardizing clinical information models called "pragmatic standardization". It involves gradually standardizing key clinical concepts over time with input from healthcare professionals. The goal is to standardize only information that needs to be reused or shared, doing so in a way that is practical for clinical work and accounts for the changing nature of healthcare. Clinician engagement is prioritized by making participation easy and demonstrating how standards can benefit patient care.
This document discusses pragmatic standardization of clinical models. It describes Norway's efforts to standardize clinical information using openEHR since 2014. Key principles of clinical modeling include having healthcare professionals define models, ensuring models can change over time, maintaining model independence from vendors, and modeling concepts once and sharing freely. Pragmatic standardization means gradual, step-by-step processes with constant maintenance rather than infrequent large revisions. Clinician engagement requires making participation quick and easy and giving clinicians resources they need. Only information meant for reuse or sharing across contexts needs to be standardized.
Presentasjon fra DIPS Forum 2017: Høring og godkjenning av arketyper er et standardiseringsarbeid, og standardiseringsarbeid tar tid. Implementasjonsprosjekter har ofte ikke dette med i tidsplanen, og dette misforholdet fører til forsinkelser. Men kan man gjøre arketypene gode nok til at det ikke fører til store problemer å ta dem i bruk før de er ferdig godkjente?
Andre næringer som f.eks. varehandel og banksektoren tar i bruk moderne IT-løsninger i høyt tempo, mens helsesektoren ser ut til å stå i stampe. Dette har sannsynligvis mange årsaker, men er det noe ved helseinformasjon i seg selv som gjør e-helse spesielt vanskelig, og hva kan vi i så fall gjøre med det?
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These lecture slides, by Dr Sidra Arshad, offer a quick overview of the physiological basis of a normal electrocardiogram.
Learning objectives:
1. Define an electrocardiogram (ECG) and electrocardiography
2. Describe how dipoles generated by the heart produce the waveforms of the ECG
3. Describe the components of a normal electrocardiogram of a typical bipolar lead (limb II)
4. Differentiate between intervals and segments
5. Enlist some common indications for obtaining an ECG
6. Describe the flow of current around the heart during the cardiac cycle
7. Discuss the placement and polarity of the leads of electrocardiograph
8. Describe the normal electrocardiograms recorded from the limb leads and explain the physiological basis of the different records that are obtained
9. Define mean electrical vector (axis) of the heart and give the normal range
10. Define the mean QRS vector
11. Describe the axes of leads (hexagonal reference system)
12. Comprehend the vectorial analysis of the normal ECG
13. Determine the mean electrical axis of the ventricular QRS and appreciate the mean axis deviation
14. Explain the concepts of current of injury, J point, and their significance
Study Resources:
1. Chapter 11, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 9, Human Physiology - From Cells to Systems, Lauralee Sherwood, 9th edition
3. Chapter 29, Ganong’s Review of Medical Physiology, 26th edition
4. Electrocardiogram, StatPearls - https://www.ncbi.nlm.nih.gov/books/NBK549803/
5. ECG in Medical Practice by ABM Abdullah, 4th edition
6. Chapter 3, Cardiology Explained, https://www.ncbi.nlm.nih.gov/books/NBK2214/
7. ECG Basics, http://www.nataliescasebook.com/tag/e-c-g-basics
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Overall life span (LS) was 1671.7±1721.6 days and cumulative 5YS reached 62.4%, 10 years – 50.4%, 20 years – 44.6%. 94 LCP lived more than 5 years without cancer (LS=2958.6±1723.6 days), 22 – more than 10 years (LS=5571±1841.8 days). 67 LCP died because of LC (LS=471.9±344 days). AT significantly improved 5YS (68% vs. 53.7%) (P=0.028 by log-rank test). Cox modeling displayed that 5YS of LCP significantly depended on: N0-N12, T3-4, blood cell circuit, cell ratio factors (ratio between cancer cells-CC and blood cells subpopulations), LC cell dynamics, recalcification time, heparin tolerance, prothrombin index, protein, AT, procedure type (P=0.000-0.031). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and N0-12 (rank=1), thrombocytes/CC (rank=2), segmented neutrophils/CC (3), eosinophils/CC (4), erythrocytes/CC (5), healthy cells/CC (6), lymphocytes/CC (7), stick neutrophils/CC (8), leucocytes/CC (9), monocytes/CC (10). Correct prediction of 5YS was 100% by neural networks computing (error=0.000; area under ROC curve=1.0).
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3. An ongoing problem…
“In attempting to arrive at the truth, I have applied
everywhere for information but in scarcely an instance have I
been able to obtain hospital records fit for any purpose of
comparison.”
“If they could be obtained, they would enable us to decide
many other questions besides the one alluded to. They would
show subscribers how their money was being spent, what
amount of good was really being done with it or whether the
money was not doing mischief rather than good.”
- Florence Nightingale, 1863
Credit: Heather Leslie
4. Why is health IT so hard?
•Banks are acing it; why isn’t health?
–Complex and dynamic domain
–Lifelong records
–Clinical diversity
–Confidentiality
–Mobile population
Credit: Heather Leslie
5. Complexity
•Both the number of concepts and the rate of
change is high
•Health is big, and continually growing…
–In breadth
–In depth
–In complexity
•Clinical knowledge is
continually changing
Credit: Heather Leslie
6. How have we been dealing with this?
•Free text(Specialist and administrative systems have more
structured data, but generic electronic health records
are still mainly free text)
7. So what do we need structure for?
•Avoid repetition and shadow records
•Retrieval and overview
•Reuse of record info
•Clinical decision support
•Quality indicators
•Management data
8. Longitudinal information access
•How long are you planning to live?
•Do you expect your health record to survive
that long?
•Even if it does survive, will
it be readable for future
systems and users?
Credit: Ricardo Correia
9. Celsius
Ear measurement
IR aural thermometer
Environment: 5° C
Wet clothing Space blanket
temperatureBody
Structuring health is hard
Credit: Bjørn Næss
10. Structuring identically is even harder
Example: Smoking status in
national registries:
• 9 different variations on
“Smoking status” in 26
different forms
• Additionally: number of cigs
per day, month quit smoking,
number of months since
quitting date, etc.
Brandt, Linn (2016). Report from REGmap February 2016 – Complete mapped register set - Preliminary analysis.
11. Structure is not the Messiah
•Structured data is not a goal in itself
•Structure where clear value can be identified
•It must be possible to add nuances using free text
•Sometimes free text
is adequate/best
suited for purpose
1
12. Semantic interoperability
•[…] the ability of computer systems
to exchange data with unambiguous,
shared meaning
•A Holy Grail of health informatics
•Requires (amongst other things)
shared information models
and terminologies
1
NCOIC, "SCOPE", Network Centric Operations Industry Consortium, 2008
13. «Information model»?
•A definition of the structure and content of the
information that should be collected or shared
– A "minimal dataset"
– A message or interface definition
•Internally all applications have some sort of
information model
•Sharing information requires developing shared
information models
Credit: Ian McNicoll
14. How have we been doing infomodelling?
•Locked into each product
•In ways that clinicians don’t understand
•Few clinicians participating
•Technicians are left to interpret
•New requirements?
16. Semantic interoperability* requires
identical data models
Clinical information modelling is difficult and
expensive, and should be done once
⇒ Information models should be
shared and governed strictly
* Level 4 semantic interoperability; Walker et al. (2005); http://www.ncbi.nlm.nih.gov/pubmed/15659453
17.
18. National governance
•Managed by Nasjonal IKT
•Goal: Sharing quality information models
•Online collaboration tools:
–http://arketyper.no
–https://kilden.sykehusene.no/display/KLIM/
•More than 400 clinicians and health informaticians
participating
1
19. • Specification for structured health records
• openEHR Foundation (openehr.org)
• Free (as in beer AND speech)
• International community
• Two level modelling
• Not an open source application
• Not a downloadable app
Illustration: https://wolandscat.net/2011/05/05/no-single-information-model/
20. openEHR reference model
• EHR structure
• Security
• Versioning
• Participants, dates/times,
data types
NO CONTENT
Credit: Heather Leslie
22. Archetypes
• Implementable specification for one clinical concept
• Comprehensible for non-techies
• Maximum datasets (aspirational)
• Reusable
THE STANDARDISED CONTENT
Credit: Heather Leslie
24. Templates
• Combinations of constrained archetypes
• Data sets for forms, messages, interfaces, etc
• For specific use cases
• NOT user interfaces
THE USECASE SPECIFIC CONTENT
Credit: Heather Leslie
26. Are information models enough?
•Sure, if we’re okay with making 100k models,
one for each diagnosis, lab result, symptom, …
•Sure, if we never want a list of all the patients
who had viral lung diseases
•We need something more: Terminologies
3
27. Terms/knowledge about
health and healthcare:
Terminologies
Vocabularies,
classifications,
ontologies; ICD-10,
SNOMED CT, ICF
Framework for information
about single individuals:
Information
models
Information structure;
openEHR archetypes, FHIR
resources
Rules to be applied to
recorded information:
Inference models
Rules and knowledge bases
used in decision support
and alert systems.
Some overlap
The things that actually
happen in healthcare:
Process models
33. Terminologies vs information models
Information models can be said to
describe the "questions"
Terminologies can give (some of) the
"answers"
Complementary concepts
ICD_10::L40.0::Psoriasis vulgaris
and
SCT_2015::74757004::Skin structure of elbow
SCT_2015::6736007::Moderate
???
34. Where terminologies shine
•Hundreds of thousands of concepts
–Diagnoses, symptoms, lab results,
body structures, organisms, procedures, …
•Inference based on relations between concepts
3
38. Context
• "Let’s just chuck the codes
in here so we can bill for this
cancer treatment!"
• 15 years later, from the brand new Dr. Google:
– "Ma’am, I’m sorry to tell you you have ovarian cancer."
– "What!? They were taken out 15 years ago!”
• Diagnosis code had no date to show when it was valid…
4
39. Quantitative data types
•«Wouldn’t it be really nice to just have a code
for the number of the pregnancy the woman is
in…?"
•"Yeah. 10 ought to be
enough for anybody."
Famous last words…
4
40. Complex concepts
•Combinatorial explosion
–"Every kind of rash for every skin area"
–Every combination of oral glucose challenge
⇒ 601 LOINC "glucose" codes:
•Postcoordination may
mitigate, but beware…
4
41. Grey areas
•Small value sets
•Some contextual information
–Actual diagnosis vs. tentative vs. risk vs. exclusion
vs. family history
•Consistent use is hard, and not always appropriate
–Different use cases will have different requirements
4
42. Summary
• Structure is important, but not always appropriate
• Clinicians must drive clinical modelling
• Information models must be shared
• Terminologies are necessary additions to information models
• Grey areas -> pragmatic choice based on requirements
More info:
• Videos of one day seminar in Sweden 2015: http://goo.gl/6Ibbkf