Eos and OMOCL: Towards a seamless integration of openEHR records into the OMOP Common Data Model.

Background: The reuse of data from electronic health records (EHRs) for research purposes promises to improve the data foundation for clinical trials and may even support to enable them. Nevertheless, EHRs are characterized by both, heterogeneous structure and semantics. To standardize this data for research, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) standard has recently seen an increase in use.

Molecular profile in Paraguayan colorectal cancer patients, towards to a precision medicine strategy.

Somatic mutation analysis and evaluation of microsatellite instability (MSI) have become mandatory for selecting personalized therapy strategies for advanced colorectal cancer and are not available as routine methods in Paraguay. The aims of this study were to analyze the molecular profile as well as the microsatellite status in a series of advanced colorectal patients from two public hospitals from Paraguay, to introduce these methodologies in the routine practice to guide the therapeutic decisions. Thirty-six patients diagnosed with advanced colorectal cancer from two referent public hospitals from Paraguay were recruited from May 2017 to February 2018.

A Standardized and Data Quality Assessed Maternal-Child Care Integrated Data Repository for Research and Monitoring of Best Practices: A Pilot Project in Spain.

We present the results of a pilot project of the Spanish Ministry of Health, Social Services and Equality, envisaged to the development of a national integrated data repository of maternal-child care information. Based on health information standards and data quality assessment procedures, the developed repository is aimed to a reliable data reuse for (1) population research and (2) the monitoring of healthcare best practices. Data standardization was provided by means of two main ISO 13606 archetypes (composed of 43 sub-archetypes), the first dedicated to the delivery and birth information and the second about the infant feeding information from delivery up to two years.

A platform for exploration into chaining of web services for clinical data transformation and reasoning.

The heterogeneity of clinical data is a key problem in the sharing and reuse of Electronic Health Record (EHR) data. We approach this problem through the combined use of EHR standards and semantic web technologies, concretely by means of clinical data transformation applications that convert EHR data in proprietary format, first into clinical information models based on archetypes, and then into RDF/OWL extracts which can be used for automated reasoning. In this paper we describe a proof-of-concept platform to facilitate the (re)configuration of such clinical data transformation applications.

Combining Archetypes with Fast Health Interoperability Resources in Future-proof Health Information Systems.

Messaging standards, and specifically HL7 v2, are heavily used for the communication and interoperability of Health Information Systems. HL7 FHIR was created as an evolution of the messaging standards to achieve semantic interoperability. FHIR is somehow similar to other approaches like the dual model methodology as both are based on the precise modeling of clinical information.

Automatic generation of computable implementation guides from clinical information models.

Clinical information models are increasingly used to describe the contents of Electronic Health Records. Implementation guides are a common specification mechanism used to define such models. They contain, among other reference materials, all the constraints and rules that clinical information must obey.

Isosemantic rendering of clinical information using formal ontologies and RDF.

The generation of a semantic clinical infostructure requires linking ontologies, clinical models and terminologies [1]. Here we describe an approach that would permit data coming from different sources and represented in different standards to be queried in a homogeneous and integrated way. Our assumption is that data providers should be able to agree and share the meaning of the data they want to exchange and to exploit.

Genetic testing information standardization in HL7 CDA and ISO13606.

Communicating genetic testing reports of a patient in a semantically interoperable way remains difficult. Most of the information is stored as non-communicable documents which cannot automatically be processed. The objective of the project was to obtain semantically interoperable genetic testing reports which could be used not only for communication purposes but also for secondary uses, for example clinical trials or clinical decision support.

Interoperability of clinical decision-support systems and electronic health records using archetypes: a case study in clinical trial eligibility.

Clinical decision-support systems (CDSSs) comprise systems as diverse as sophisticated platforms to store and manage clinical data, tools to alert clinicians of problematic situations, or decision-making tools to assist clinicians. Irrespective of the kind of decision-support task CDSSs should be smoothly integrated within the clinical information system, interacting with other components, in particular with the electronic health record (EHR). However, despite decades of developments, most CDSSs lack interoperability features.

Using the ResearchEHR platform to facilitate the practical application of the EHR standards.

Possibly the most important requirement to support co-operative work among health professionals and institutions is the ability of sharing EHRs in a meaningful way, and it is widely acknowledged that standardization of data and concepts is a prerequisite to achieve semantic interoperability in any domain. Different international organizations are working on the definition of EHR architectures but the lack of tools that implement them hinders their broad adoption. In this paper we present ResearchEHR, a software platform whose objective is to facilitate the practical application of EHR standards as a way of reaching the desired semantic interoperability.

CEN EN13606 normalisation framework implementation experiences.

Since the approval of the CEN EN13606 norm for the electronic health record communication, a growing interest around the application of this specification has emerged. The main objective of the norm is to serve as a mechanism to achieve the semantic interoperability of clinical data. This will require an effort to use common terminologies, to normalise the clinical knowledge domain and to combine all these formalisations with the existing information systems.

ResearchEHR: use of semantic web technologies and archetypes for the description of EHRs.

In this paper, we present the ResearchEHR project. It focuses on the usability of Electronic Health Record (EHR) sources and EHR standards for building advanced clinical systems. The aim is to support healthcare professional, institutions and authorities by providing a set of generic methods and tools for the capture, standardization, integration, description and dissemination of health related information.

LinkEHR-Ed: a multi-reference model archetype editor based on formal semantics.

Purpose: To develop a powerful archetype editing framework capable of handling multiple reference models and oriented towards the semantic description and standardization of legacy data.

Methods: The main prerequisite for implementing tools providing enhanced support for archetypes is the clear specification of archetype semantics. We propose a formalization of the definition section of archetypes based on types over tree-structured data.

Standardization of discharge reports with the ISO 13606 norm.

The International Organization for Standardization (ISO) has recently approved a new standard for the communication and semantic interoperability of electronic health record extracts. This standard is based on a dual model architecture, where a simple and generic reference model is defined for the representation of data and an archetype model is used for the representation of complex domain concepts of the electronic health record. By using this standard and a tool called LinkEHR-Ed, we have defined different types of hospital discharge reports in the form of archetypes and then we have normalized automatically discharge reports instances in a real environment following those archetype definitions.

Semantic upgrade and normalization of existing EHR extracts.

We present the mapping and data transformation capabilities of LinkEHR-Ed, a visual tool to construct formal definitions of medical concepts in the form of archetypes which can be defined on the basis on multiple electronic health record architecture such as ISO 13606. With LinkEHR-Ed, users can enrich archetypes with mapping information which captures the relationship between relational or XML data sources and archetype structures. This mapping information is then analyzed and compiled into an XQuery expression that transforms source instances into an XML document.

Archetype-based semantic integration and standardization of clinical data.

One of the basic needs for any healthcare professional is to be able to access to clinical information of patients in an understandable and normalized way. The lifelong clinical information of any person supported by electronic means configures his/her Electronic Health Record (EHR). This information is usually distributed among several independent and heterogeneous systems that may be syntactically or semantically incompatible.