Secondary Use Of Electronic Health Research Articles

Quality assessment of functional status documentation in EHRs across different healthcare institutions.

The secondary use of electronic health records (EHRs) faces challenges in the form of varying data quality-related issues. To address that, we retrospectively assessed the quality of functional status documentation in EHRs of persons participating in Mayo Clinic Study of Aging (MCSA). We used a convergent parallel design to collect quantitative and qualitative data and independently analyzed the findings. We discovered a heterogeneous documentation process, where the care practice teams, institutions, and EHR systems all play an important role in how text data is documented and organized. Four prevalent instrument-assisted documentation (iDoc) expressions were identified based on three distinct instruments: Epic smart form, questionnaire, and occupational therapy and physical therapy templates. We found strong differences in the usage, information quality (intrinsic and contextual), and naturality of language among different type of iDoc expressions. These variations can be caused by different source instruments, information providers, practice settings, care events and institutions. In addition, iDoc expressions are context specific and thus shall not be viewed and processed uniformly. We recommend conducting data quality assessment of unstructured EHR text prior to using the information.

Digitalization of Health Data: Interoperability of the Proposed European Health Data Space.

On May 3rd, 2022, the European Commission published its legislative proposal to create a European Health Data Space (EHDS) enabling citizens of the European Union to gain secure access to their electronic health data by establishing a market for digital health. This market will feature the primary and secondary use of electronic health records by digital products and services. The articles of the proposal address many aspects of ensuring health data interoperability. That includes the creation of a European Electronic Health Record Exchange Format for defined data categories including patient summaries and electronic prescriptions, the development of a central platform to provide a cross-border digital infrastructure and that each Member State institutes a digital health authority and a national point of contact. In addition, the Commission will define common specifications that electronic health record systems and medical devices will have to meet as interoperability requirements. In its current form, the proposal does not stipulate specific standards that need to be universally adopted to ensure semantic and syntactical interoperability. Considering that many datasets are not internationally harmonized and lack standardization, these specifications will need to be provided for example by existing standards like the International Patient Summary.

The Implication of Latent Information Quality to the Reproducibility of Secondary Use of Electronic Health Records.

Reproducibility is an important quality criterion for the secondary use of electronic health records (EHRs). However, multiple barriers to reproducibility are embedded in the heterogeneous EHR environment. These barriers include complex processes for collecting and organizing EHR data and dynamic multi-level interactions occurring during information use (e.g., inter-personal, inter-system, and cross-institutional). To ensure reproducible use of EHRs, we investigated four information quality dimensions and examine the implications for reproducibility based on a real-world EHR study. Four types of IQ measurements suggested that barriers to reproducibility occurred for all stages of secondary use of EHR data. We discussed our recommendations and emphasized the importance of promoting transparent, high-throughput, and accessible data infrastructures and implementation best practices (e.g., data quality assessment, reporting standard).

Application of openEHR archetypes to automate data quality rules for electronic health records: a case study

BackgroundEnsuring data is of appropriate quality is essential for the secondary use of electronic health records (EHRs) in research and clinical decision support. An effective method of data quality assessment (DQA) is automating data quality rules (DQRs) to replace the time-consuming, labor-intensive manual process of creating DQRs, which is difficult to guarantee standard and comparable DQA results. This paper presents a case study of automatically creating DQRs based on openEHR archetypes in a Chinese hospital to investigate the feasibility and challenges of automating DQA for EHR data.MethodsThe clinical data repository (CDR) of the Shanxi Dayi Hospital is an archetype-based relational database. Four steps are undertaken to automatically create DQRs in this CDR database. First, the keywords and features relevant to DQA of archetypes were identified via mapping them to a well-established DQA framework, Kahn’s DQA framework. Second, the templates of DQRs in correspondence with these identified keywords and features were created in the structured query language (SQL). Third, the quality constraints were retrieved from archetypes. Fourth, these quality constraints were automatically converted to DQRs according to the pre-designed templates and mapping relationships of archetypes and data tables. We utilized the archetypes of the CDR to automatically create DQRs to meet quality requirements of the Chinese Application-Level Ranking Standard for EHR Systems (CARSES) and evaluated their coverage by comparing with expert-created DQRs.ResultsWe used 27 archetypes to automatically create 359 DQRs. 319 of them are in agreement with the expert-created DQRs, covering 84.97% (311/366) requirements of the CARSES. The auto-created DQRs had varying levels of coverage of the four quality domains mandated by the CARSES: 100% (45/45) of consistency, 98.11% (208/212) of completeness, 54.02% (57/87) of conformity, and 50% (11/22) of timeliness.ConclusionIt’s feasible to create DQRs automatically based on openEHR archetypes. This study evaluated the coverage of the auto-created DQRs to a typical DQA task of Chinese hospitals, the CARSES. The challenges of automating DQR creation were identified, such as quality requirements based on semantic, and complex constraints of multiple elements. This research can enlighten the exploration of DQR auto-creation and contribute to the automatic DQA.

Evaluation of the secondary use of electronic health records to detect seasonal, holiday-related, and rare events related to traumatic injury and poisoning

BackgroundThe increasing adoption of electronic health record (EHR) systems enables automated, large scale, and meaningful analysis of regional population health. We explored how EHR systems could inform surveillance of trauma-related emergency department visits arising from seasonal, holiday-related, and rare environmental events.MethodsWe analyzed temporal variation in diagnosis codes over 24 years of trauma visit data at the three hospitals in the University of Washington Medicine system in Seattle, Washington, USA. We identified seasons and days in which specific codes and categories of codes were statistically enriched, meaning that a significantly greater than average proportion of trauma visits included a given diagnosis code during that time period.ResultsWe confirmed known seasonal patterns in emergency department visits for trauma. As expected, cold weather-related incidents (e.g. frostbite, snowboarding injury) were enriched in the winter, whereas fair weather-related incidents (e.g. bug bites, boating accidents, bicycle accidents) were enriched in the spring and summer. Our analysis of specific days of the year found that holidays were enriched for alcohol poisoning, assaults, and firework accidents. We also detected one time regional events such as the 2001 Nisqually earthquake and the 2006 Hanukkah Eve Windstorm.ConclusionsThough EHR systems were developed to prioritize operational rather than analytic priorities and have consequent limitations for surveillance, our EHR enrichment analysis nonetheless re-identified expected temporal population health patterns. EHRs are potentially a valuable source of information to inform public health policy, both in retrospective analysis and in a surveillance capacity.

Knowledge Discovery With Machine Learning for Hospital-Acquired Catheter-Associated Urinary Tract Infections.

Massive generation of health-related data has been key in enabling the big data science initiative to gain new insights in healthcare. Nursing can benefit from this era of big data science, as there is a growing need for new discoveries from large quantities of nursing data to provide evidence-based care. However, there are few nursing studies using big data analytics. The purpose of this article is to explain a knowledge discovery and data mining approach that was employed to discover knowledge about hospital-acquired catheter-associated urinary tract infections from multiple data sources, including electronic health records and nurse staffing data. Three different machine learning techniques are described: decision trees, logistic regression, and support vector machines. The decision tree model created rules to interpret relationships among associated factors of hospital-acquired catheter-associated urinary tract infections. The logistic regression model showed what factors were related to a higher risk of hospital-acquired catheter-associated urinary tract infections. The support vector machines model was included to compare performance with the other two interpretable models. This article introduces the examples of cutting-edge machine learning approaches that will advance secondary use of electronic health records and integration of multiple data sources as well as provide evidence necessary to guide nursing professionals in practice.

Feasibility analysis of conducting observational studies with the electronic health record

BackgroundThe secondary use of electronic health records (EHRs) promises to facilitate medical research. We reviewed general data requirements in observational studies and analyzed the feasibility of conducting observational studies with structured EHR data, in particular diagnosis and procedure codes.MethodsAfter reviewing published observational studies from the University Hospital of Erlangen for general data requirements, we identified three different study populations for the feasibility analysis with eligibility criteria from three exemplary observational studies. For each study population, we evaluated the availability of relevant patient characteristics in our EHR, including outcome and exposure variables. To assess data quality, we computed distributions of relevant patient characteristics from the available structured EHR data and compared them to those of the original studies. We implemented computed phenotypes for patient characteristics where necessary. In random samples, we evaluated how well structured patient characteristics agreed with a gold standard from manually interpreted free texts. We categorized our findings using the four data quality dimensions “completeness”, “correctness”, “currency” and “granularity”.ResultsReviewing general data requirements, we found that some investigators supplement routine data with questionnaires, interviews and follow-up examinations. We included 847 subjects in the feasibility analysis (Study 1 n = 411, Study 2 n = 423, Study 3 n = 13). All eligibility criteria from two studies were available in structured data, while one study required computed phenotypes in eligibility criteria. In one study, we found that all necessary patient characteristics were documented at least once in either structured or unstructured data. In another study, all exposure and outcome variables were available in structured data, while in the other one unstructured data had to be consulted. The comparison of patient characteristics distributions, as computed from structured data, with those from the original study yielded similar distributions as well as indications of underreporting. We observed violations in all four data quality dimensions.ConclusionsWhile we found relevant patient characteristics available in structured EHR data, data quality problems may entail that it remains a case-by-case decision whether diagnosis and procedure codes are sufficient to underpin observational studies. Free-text data or subsequently supplementary study data may be important to complement a comprehensive patient history.

Methodological description of clinical research data collection through electronic medical records in a center participating in an international multicenter study.

ABSTRACTData collection for clinical research can be difficult, and electronic health record systems can facilitate this process. The aim of this study was to describe and evaluate the secondary use of electronic health records in data collection for an observational clinical study. We used Cerner Millennium®, an electronic health record software, following these steps: (1) data crossing between the study’s case report forms and the electronic health record; (2) development of a manual collection method for data not recorded in Cerner Millennium®; (3) development of a study interface for automatic data collection in the electronic health records; (4) employee training; (5) data quality assessment; and (6) filling out the electronic case report form at the end of the study. Three case report forms were consolidated into the electronic case report form at the end of the study. Researchers performed daily qualitative and quantitative analyses of the data. Data were collected from 94 patients. In the first case report form, 76.5% of variables were obtained electronically, in the second, 95.5%, and in the third, 100%. The daily quality assessment of the whole process showed complete and correct data, widespread employee compliance and minimal interference in their practice. The secondary use of electronic health records is safe and effective, reduces manual labor, and provides data reliability. Anesthetic care and data collection may be done by the same professional.

Patient Perspectives About Decisions to Share Medical Data and Biospecimens for Research

Patients increasingly demand transparency in and control of how their medical records and biospecimens are shared for research. How much they are willing to share and what factors influence their sharing preferences remain understudied in real settings. To examine whether and how various presentations of consent forms are associated with differences in electronic health record and biospecimen sharing rates and whether these rates vary according to user interface design, data recipients, data and biospecimen items, and patient characteristics. For this survey study, a data and biospecimen sharing preference survey was conducted at 2 academic hospitals from May 1, 2017, to September 31, 2018, after simple randomization of patients to 1 of 4 options with different layout and formats of indicating sharing preferences: opt-in simple, opt-in detailed, opt-out simple, and opt-out detailed. All participants were presented with a list of data and biospecimen items that could be shared for research within the same health care organization or with other nonprofit or for-profit institutions. Participating patients were randomly asked to select the items that they would share (opt-in) or were asked to select items they would not share (opt-out). Patients in these 2 groups were further randomized to select only among 18 categories vs 59 detailed items (simple vs detailed form layout). The primary end points were the percentages of patients willing to share data and biospecimen categories or items. Among 1800 eligible participants, 1246 (69.2%) who completed their data sharing survey were included in the analysis, and 850 of these patients (mean [SD] age, 51.1 [16.7] years; 507 [59.6%] female; 677 [79.6%] white) responded to the satisfaction survey. A total of 46 participants (3.7%) declined sharing with the home institution, 352 (28.3%) with nonprofit institutions, and 590 (47.4%) with for-profit institutions. A total of 836 (67.1%) indicated that they would share all items with researchers from the home institution. When comparing opt-out with opt-in interfaces, all 59 sharing choice variables (100%) were associated with the sharing decision. When comparing simple with detailed forms, only 14 variables (23.7%) were associated with the sharing decision. The findings suggest that most patients are willing to share their data and biospecimens for research. Allowing patients to decide with whom they want to share certain types of data may affect research that involves secondary use of electronic health records and/or biosamples for research.

Development and implementation of a dynamically updated big data intelligence platform from electronic health records for nasopharyngeal carcinoma research.

To develop a big data intelligence platform for secondary use of electronic health records (EHRs) data to facilitate research for nasopharyngeal cancer (NPC). This project was launched in 2015 and carried out by the cooperation of an academic cancer centre and a technology company. Patients diagnosed with NPC at Sun Yat-sen University Cancer Centre since January 2008 were included in the platform. Standard data elements were established to defined 981 variables for the platform. For each patient, data from 13 EHRs systems were extracted, integrated, structurized and normalized. Eight functional modules were constructed for the platform to facilitate the investigators to identify eligible patients, establish research projects, conduct statistical analysis, track the follow-up, search literature, etc. From January 2008 to December 2018, 54,703 patients diagnosed with NPC were included. Of these patients, 39,058 (71.4%) were male, and 15,645 (28.6%) were female; median age was 47 (interquartile range, 39-55) years. Of 981 variables, 341 were obtained from data structurization and normalization, of which 68 were generated by interacting multiple data sources via well-defined logical rules. The average precision rate, recall rate and F-measure for 341 variables were 0.97 ± 0.024, 0.92 ± 0.030, and 0.94 ± 0.027 respectively. The platform is regularly updated every seven days to include new patients and add new data for existing patients. Up to now, eight big data-driven retrospective studies have been published from the platform. Our big data intelligence platform demonstrates the feasibility of integrating EHRs data of routine healthcare, and offers an important perspective on real-world study of NPC. The continued efforts may be focus on data sharing among multiple hospitals and publicly releasing of data files. Our big data intelligence platform is the first disease-specific data platform for NPC research. It incorporates comprehensive EHRs data from routine healthcare, which can facilitate real-world study of NPC in risk stratification, decision-making and comorbidities management.

Gathering data for decisions: best practice use of primary care electronic records for research.

Summary In Australia, there is limited use of primary health care data for research and for data linkage between health care settings. This puts Australia behind many developed countries. In addition, without use of primary health care data for research, knowledge about patients’ journeys through the health care system is limited.There is growing momentum to establish “big data” repositories of primary care clinical data to enable data linkage, primary care and population health research, and quality assurance activities. However, little research has been conducted on the general public's and practitioners’ concerns about secondary use of electronic health records in Australia.International studies have identified barriers to use of general practice patient records for research. These include legal, technical, ethical, social and resource‐related issues. Examples include concerns about privacy protection, data security, data custodians and the motives for collecting data, as well as a lack of incentives for general practitioners to share data.Addressing barriers may help define good practices for appropriate use of health data for research. Any model for general practice data sharing for research should be underpinned by transparency and a strong legal, ethical, governance and data security framework.Mechanisms to collect electronic medical records in ethical, secure and privacy‐controlled ways are available.Before the potential benefits of health‐related data research can be realised, Australians should be well informed of the risks and benefits so that the necessary social licence can be generated to support such endeavours.

Secondary use of electronic health records: Availability aspects in two Nordic countries

The potential for the secondary use of electronic health records (EHRs) is underused due to restrictions in national legislation. For privacy purposes, legislative restrictions limit the availability and content of EHR data provided to secondary users. These limitations do not encourage healthcare organisations to develop procedures to promote the secondary use of EHRs. The objective of this study is to identify factors that restrict the secondary use of unstructured EHRs in academic research in Finland and Sweden. A study was conducted to identify these availability-restricting issues that pertain to the academic secondary use of unstructured EHRs. Using semi-structured interviews, 14 domain experts in science, hospital management and business were interviewed to evaluate the efficiency of procedures and technologies that are implemented in secondary use processes. The results demonstrate three aspects that restrict the availability of unstructured EHRs for secondary purposes: (i) the management and (ii) privacy preservation of such data as well as (iii) potential secondary users. Based on these categories, two approaches for the secondary use of unstructured EHRs are identified: the protected processing environment and altered data. The protected processing environment ensures patient privacy by providing unstructured EHRs for exclusive user groups that have preferred use intentions. Compared to the use of such processing environments, data alteration enables the secondary use of unstructured EHRs for a larger user group with various use intentions but that yield less valuable content.

Preliminary exploration of survival analysis using the OHDSI common data model: a case study of intrahepatic cholangiocarcinoma

BackgroundData heterogeneity is a common phenomenon related to the secondary use of electronic health records (EHR) data from different sources. The Observational Health Data Sciences and Informatics (OHDSI) Common Data Model (CDM) organizes healthcare data into standard data structures using concepts that are explicitly and formally specified through standard vocabularies, thereby facilitating large-scale analysis. The objective of this study is to design, develop, and evaluate generic survival analysis routines built using the OHDSI CDM.MethodsWe used intrahepatic cholangiocarcinoma (ICC) patient data to implement CDM-based survival analysis methods. Our methods comprise the following modules: 1) Mapping local terms to standard OHDSI concepts. The analytical expression of variables and values related to demographic characteristics, medical history, smoking status, laboratory results, and tumor feature data. These data were mapped to standard OHDSI concepts through a manual analysis; 2) Loading patient data into the CDM using the concept mappings; 3) Developing an R interface that supports the portable survival analysis on top of OHDSI CDM, and comparing the CDM-based analysis results with those using traditional statistical analysis methods.ResultsOur dataset contained 346 patients diagnosed with ICC. The collected clinical data contains 115 variables, of which 75 variables were mapped to the OHDSI concepts. These concepts mainly belong to four domains: condition, observation, measurement, and procedure. The corresponding standard concepts are scattered in six vocabularies: ICD10CM, ICD10PCS, SNOMED, LOINC, NDFRT, and READ. We loaded a total of 25,950 patient data records into the OHDSI CDM database. However, 40 variables failed to map to the OHDSI CDM as they mostly belong to imaging data and pathological data.ConclusionsOur study demonstrates that conducting survival analysis using the OHDSI CDM is feasible and can produce reusable analysis routines. However, challenges to be overcome include 1) semantic loss caused by inaccurate mapping and value normalization; 2) incomplete OHDSI vocabularies describing imaging data, pathological data, and modular data representation.

Diabetes and the direct secondary use of electronic health records: Using routinely collected and stored data to drive research and understanding.

IntroductionElectronic health records provide an unparalleled opportunity for the use of patient data that is routinely collected and stored, in order to drive research and develop an epidemiological understanding of disease. Diabetes, in particular, stands to benefit, being a data-rich, chronic-disease state. This article aims to provide an understanding of the extent to which the healthcare sector is using routinely collected and stored data to inform research and epidemiological understanding of diabetes mellitus.MethodsNarrative literature review of articles, published in both the medical- and engineering-based informatics literature.ResultsThere has been a significant increase in the number of papers published, which utilise electronic health records as a direct data source for diabetes research. These articles consider a diverse range of research questions. Internationally, the secondary use of electronic health records, as a research tool, is most prominent in the USA. The barriers most commonly described in research studies include missing values and misclassification, alongside challenges of establishing the generalisability of results.DiscussionElectronic health record research is an important and expanding area of healthcare research. Much of the research output remains in the form of conference abstracts and proceedings, rather than journal articles. There is enormous opportunity within the United Kingdom to develop these research methodologies, due to national patient identifiers. Such a healthcare context may enable UK researchers to overcome many of the barriers encountered elsewhere and thus to truly unlock the potential of electronic health records.

Electronic Health Record Driven Prediction for Gestational Diabetes Mellitus in Early Pregnancy

Gestational diabetes mellitus (GDM) is conventionally confirmed with oral glucose tolerance test (OGTT) in 24 to 28 weeks of gestation, but it is still uncertain whether it can be predicted with secondary use of electronic health records (EHRs) in early pregnancy. To this purpose, the cost-sensitive hybrid model (CSHM) and five conventional machine learning methods are used to construct the predictive models, capturing the future risks of GDM in the temporally aggregated EHRs. The experimental data sources from a nested case-control study cohort, containing 33,935 gestational women in West China Second Hospital. After data cleaning, 4,378 cases and 50 attributes are stored and collected for the data set. Through selecting the most feasible method, the cost parameter of CSHM is adapted to deal with imbalance of the dataset. In the experiment, 3940 samples are used for training and the rest 438 samples for testing. Although the accuracy of positive samples is barely acceptable (62.16%), the results suggest that the vast majority (98.4%) of those predicted positive instances are real positives. To our knowledge, this is the first study to apply machine learning models with EHRs to predict GDM, which will facilitate personalized medicine in maternal health management in the future.

Clinical Research Informatics Contributions from 2015.

To summarize key contributions to current research in the field of Clinical Research Informatics (CRI) and to select best papers published in 2015. A bibliographic search using a combination of MeSH and free terms search over PubMed on Clinical Research Informatics (CRI) was performed followed by a double-blind review in order to select a list of candidate best papers to be then peer-reviewed by external reviewers. A consensus meeting between the two section editors and the editorial team was finally organized to conclude on the selection of best papers. Among the 579 returned papers published in the past year in the various areas of Clinical Research Informatics (CRI) - i) methods supporting clinical research, ii) data sharing and interoperability, iii) re-use of healthcare data for research, iv) patient recruitment and engagement, v) data privacy, security and regulatory issues and vi) policy and perspectives - the full review process selected four best papers. The first selected paper evaluates the capability of the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM) to support the representation of case report forms (in both the design stage and with patient level data) during a complete clinical study lifecycle. The second selected paper describes a prototype for secondary use of electronic health records data captured in non-standardized text. The third selected paper presents a privacy preserving electronic health record linkage tool and the last selected paper describes how big data use in US relies on access to health information governed by varying and often misunderstood legal requirements and ethical considerations. A major trend in the 2015 publications is the analysis of observational, "nonexperimental" information and the potential biases and confounding factors hidden in the data that will have to be carefully taken into account to validate new predictive models. In addiction, researchers have to understand complicated and sometimes contradictory legal requirements and to consider ethical obligations in order to balance privacy and promoting discovery.

Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records.

Secondary use of electronic health records (EHRs) promises to advance clinical research and better inform clinical decision making. Challenges in summarizing and representing patient data prevent widespread practice of predictive modeling using EHRs. Here we present a novel unsupervised deep feature learning method to derive a general-purpose patient representation from EHR data that facilitates clinical predictive modeling. In particular, a three-layer stack of denoising autoencoders was used to capture hierarchical regularities and dependencies in the aggregated EHRs of about 700,000 patients from the Mount Sinai data warehouse. The result is a representation we name “deep patient”. We evaluated this representation as broadly predictive of health states by assessing the probability of patients to develop various diseases. We performed evaluation using 76,214 test patients comprising 78 diseases from diverse clinical domains and temporal windows. Our results significantly outperformed those achieved using representations based on raw EHR data and alternative feature learning strategies. Prediction performance for severe diabetes, schizophrenia, and various cancers were among the top performing. These findings indicate that deep learning applied to EHRs can derive patient representations that offer improved clinical predictions, and could provide a machine learning framework for augmenting clinical decision systems.

Bridging data models and terminologies to support adverse drug event reporting using EHR data.

This article is part of the Focus Theme of METHODs of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". SALUS project aims at building an interoperability platform and a dedicated toolkit to enable secondary use of electronic health records (EHR) data for post marketing drug surveillance. An important component of this toolkit is a drug-related adverse events (AE) reporting system designed to facilitate and accelerate the reporting process using automatic prepopulation mechanisms. To demonstrate SALUS approach for establishing syntactic and semantic interoperability for AE reporting. Standard (e.g. HL7 CDA-CCD) and proprietary EHR data models are mapped to the E2B(R2) data model via SALUS Common Information Model. Terminology mapping and terminology reasoning services are designed to ensure the automatic conversion of source EHR terminologies (e.g. ICD-9-CM, ICD-10, LOINC or SNOMED-CT) to the target terminology MedDRA which is expected in AE reporting forms. A validated set of terminology mappings is used to ensure the reliability of the reasoning mechanisms. The percentage of data elements of a standard E2B report that can be completed automatically has been estimated for two pilot sites. In the best scenario (i.e. the available fields in the EHR have actually been filled), only 36% (pilot site 1) and 38% (pilot site 2) of E2B data elements remain to be filled manually. In addition, most of these data elements shall not be filled in each report. SALUS platform's interoperability solutions enable partial automation of the AE reporting process, which could contribute to improve current spontaneous reporting practices and reduce under-reporting, which is currently one major obstacle in the process of acquisition of pharmacovigilance data.

Secondary use of electronic health records for building cohort studies through top-down information extraction

Controlled clinical trials are usually supported with an in-front data aggregation system, which supports the storage of relevant information according to the trial context within a highly structured environment. In contrast to the documentation of clinical trials, daily routine documentation has many characteristics that influence data quality. One such characteristic is the use of non-standardized text, which is an indispensable part of information representation in clinical information systems. Based on a cohort study we highlight challenges for mining electronic health records targeting free text entry fields within semi-structured data sources. Our prototypical information extraction system achieved an F-measure of 0.91 (precision=0.90, recall=0.93) for the training set and an F-measure of 0.90 (precision=0.89, recall=0.92) for the test set. We analyze the obtained results in detail and highlight challenges and future directions for the secondary use of routine data in general.

A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data

The clinical element model (CEM) is an information model designed for representing clinical information in electronic health records (EHR) systems across organizations. The current representation of CEMs does not support formal semantic definitions and therefore it is not possible to perform reasoning and consistency checking on derived models. This paper introduces our efforts to represent the CEM specification using the Web Ontology Language (OWL). The CEM-OWL representation connects the CEM content with the Semantic Web environment, which provides authoring, reasoning, and querying tools. This work may also facilitate the harmonization of the CEMs with domain knowledge represented in terminology models as well as other clinical information models such as the openEHR archetype model. We have created the CEM-OWL meta ontology based on the CEM specification. A convertor has been implemented in Java to automatically translate detailed CEMs from XML to OWL. A panel evaluation has been conducted, and the results show that the OWL modeling can faithfully represent the CEM specification and represent patient data.