Semantic Metadata Annotation Services in the Biomedical Domain—A Literature Review

For all research data collected, data descriptions and information about the corresponding variables are essential for data analysis and reuse. To enable cross-study comparisons and analyses, semantic interoperability of metadata is one of the most important requirements. In the area of clinical and epidemiological studies, data collection instruments such as case report forms (CRFs), data dictionaries and questionnaires are critical for metadata collection. Even though data collection instruments are often created in a digital form, they are mostly not machine readable; i.e., they are not semantically coded. As a result, the comparison between data collection instruments is complex. The German project NFDI4Health is dedicated to the development of national research data infrastructure for personal health data, and as such searches for ways to enhance semantic interoperability. Retrospective integration of semantic codes into study metadata is important, as ongoing or completed studies contain valuable information. However, this is labor intensive and should be eased by software. To understand the market and find out what techniques and technologies support retrospective semantic annotation/enrichment of metadata, we conducted a literature review. In NFDI4Health, we identified basic requirements for semantic metadata annotation software in the biomedical field and in the context of the FAIR principles. Ten relevant software systems were summarized and aligned with those requirements. We concluded that despite active research on semantic annotation systems, no system meets all requirements. Consequently, further research and software development in this area is needed, as interoperability of data dictionaries, questionnaires and data collection tools is key to reusing and combining results from independent research studies.

Facilitating Semantic Interoperability of Trustworthy IoT Entities in Cultural Spaces: The Smart Museum Ontology

Nowadays, cultural spaces (e.g., museums and archaeological sites) are interested in adding intelligence in their ecosystem by deploying different types of smart applications such as automated environmental monitoring, energy saving, and user experience optimization. Such an ecosystem is better realized through semantics in order to efficiently represent the required knowledge for facilitating interoperability among different application domains, integration of data, and inference of new knowledge as insights into what may have not been observed at first sight. This paper reports on our recent efforts for the engineering of a smart museum (SM) ontology that meets the following objectives: (a) represent knowledge related to trustworthy IoT entities that “live” and are deployed in a SM, i.e., things, sensors, actuators, people, data, and applications; (b) deal with the semantic interoperability and integration of heterogeneous SM applications and data; (c) represent knowledge related to museum visits and visitors toward enhancing their visiting experience; (d) represent knowledge related to smart energy saving; (e) represent knowledge related to the monitoring of environmental conditions in museums; and (f) represent knowledge related to the space and location of exhibits and collections. The paper not only contributes a novel SM ontology, but also presents the updated HCOME methodology for the agile, human-centered, collaborative and iterative engineering of living, reused, and modular ontologies.

Mapping of OpenEHR Archetypes to FHIR Resources in Use Case Oncology

Unambiguous data exchange among healthcare systems is essential for error-free reporting and improved patient care. Mapping of different standards plays a crucial role in making different systems communicate with each other and have an efficient healthcare systems. This work focuses on exploring the possibilities of semantic interoperability between two widely used clinical modelling standards, OpenEHR and FHIR (Fast Healthcare Interoperability Resources). A manually curated map is being developed where the same semantically meaning OpenEHR Archetypes are mapped to the relevant FHIR Resources.

Verifying the Feasibility of Implementing Semantic Interoperability in Different Countries Based on the OpenEHR Approach: Comparative Study of Acute Coronary Syndrome Registries

Background The semantic interoperability of health care information has been a critical challenge in medical informatics and has influenced the integration, sharing, analysis, and use of medical big data. International standard organizations have developed standards, approaches, and models to improve and implement semantic interoperability. The openEHR approach—one of the standout semantic interoperability approaches—has been implemented worldwide to improve semantic interoperability based on reused archetypes. Objective This study aimed to verify the feasibility of implementing semantic interoperability in different countries by comparing the openEHR-based information models of 2 acute coronary syndrome (ACS) registries from China and New Zealand. Methods A semantic archetype comparison method was proposed to determine the semantics reuse degree of reused archetypes in 2 ACS-related clinical registries from 2 countries. This method involved (1) determining the scope of reused archetypes; (2) identifying corresponding data items within corresponding archetypes; (3) comparing the semantics of corresponding data items; and (4) calculating the number of mappings in corresponding data items and analyzing results. Results Among the related archetypes in the two ACS-related, openEHR-based clinical registries from China and New Zealand, there were 8 pairs of reusable archetypes, which included 89 pairs of corresponding data items and 120 noncorresponding data items. Of the 89 corresponding data item pairs, 87 pairs (98%) were mappable and therefore supported semantic interoperability, and 71 pairs (80%) were labeled as “direct mapping” data items. Of the 120 noncorresponding data items, 114 (95%) data items were generated via archetype evolution, and 6 (5%) data items were generated via archetype localization. Conclusions The results of the semantic comparison between the two ACS-related clinical registries prove the feasibility of establishing the semantic interoperability of health care data from different countries based on the openEHR approach. Archetype reuse provides data on the degree to which semantic interoperability exists when using the openEHR approach. Although the openEHR community has effectively promoted archetype reuse and semantic interoperability by providing archetype modeling methods, tools, model repositories, and archetype design patterns, the uncontrolled evolution of archetypes and inconsistent localization have resulted in major challenges for achieving higher levels of semantic interoperability.

Providing ART-DECOR ValueSets via FHIR Terminology Servers – A Technical Report

To ensure semantic interoperability within healthcare systems, using common, curated terminological systems to identify relevant concepts is of fundamental importance. The HL7 FHIR standard specifies means of modelling terminological systems and appropriate ways of accessing and querying these artefacts within a terminology server. Hence, initiatives towards healthcare interoperability like IHE specify not only software interfaces, but also common codes in the form of value sets and code systems. The way in which these coding tables are provided is not necessarily compatible to the current version of the HL7 FHIR specification and therefore cannot be used with current HL7 FHIR-based terminology servers. This work demonstrates a conversion of terminological resources specified by the Integrating the Healthcare Initiative in the ART-DECOR platform, partly available in HL7 FHIR, to ensure that they can be used within a HL7 FHIR-based terminological server. The approach itself can be used for other terminological resources specified within ART-DECOR but can also be used as the basis for other code-driven conversions of proprietary coding schemes.

The Pipeline for Standardizing Russian Unstructured Allergy Anamnesis Using FHIR AllergyIntolerance Resource

Background The larger part of essential medical knowledge is stored as free text which is complicated to process. Standardization of medical narratives is an important task for data exchange, integration, and semantic interoperability. Objectives The article aims to develop the end-to-end pipeline for structuring Russian free-text allergy anamnesis using international standards. Methods The pipeline for free-text data standardization is based on FHIR (Fast Healthcare Interoperability Resources) and SNOMED CT (Systematized Nomenclature of Medicine Clinical Terms) to ensure semantic interoperability. The pipeline solves common tasks such as data preprocessing, classification, categorization, entities extraction, and semantic codes assignment. Machine learning methods, rule-based, and dictionary-based approaches were used to compose the pipeline. The pipeline was evaluated on 166 randomly chosen medical records. Results AllergyIntolerance resource was used to represent allergy anamnesis. The module for data preprocessing included the dictionary with over 90,000 words, including specific medication terms, and more than 20 regular expressions for errors correction, classification, and categorization modules resulted in four dictionaries with allergy terms (total 2,675 terms), which were mapped to SNOMED CT concepts. F-scores for different steps are: 0.945 for filtering, 0.90 to 0.96 for allergy categorization, 0.90 and 0.93 for allergens reactions extraction, respectively. The allergy terminology coverage is more than 95%. Conclusion The proposed pipeline is a step to ensure semantic interoperability of Russian free-text medical records and could be effective in standardization systems for further data exchange and integration.

RML based ontology development approach in internet of things for healthcare domain

Purpose A huge amount of diverse data is generated in the Internet of Things (IoT) because of heterogeneous devices like sensors, actuators, gateways and many more. Due to assorted nature of devices, interoperability remains a major challenge for IoT system developers. The purpose of this study is to use mapping techniques for converting relational database (RDB) to resource directory framework (RDF) for the development of ontology. Ontology helps in achieving semantic interoperability in application areas of IoT which results in shared/common understanding of the heterogeneous data generated by the diverse devices used in health-care domain. Design/methodology/approach To overcome the issue of semantic interoperability in healthcare domain, the authors developed an ontology for patients having cardio vascular diseases. Patients located at any place around the world can be diagnosed by Heart Experts located at another place by using this approach. This mechanism deals with the mapping of heterogeneous data into the RDF format in an integrated and interoperable manner. This approach is used to integrate the diverse data of heart patients needed for diagnosis with respect to cardio vascular diseases. This approach is also applicable in other fields where IoT is mostly used. Findings Experimental results showed that the RDF works better than the relational database for semantic interoperability in the IoT. This concept-based approach is better than key-based approach and reduces the computation time and storage of the data. Originality/value The proposed approach helps in overcoming the demerits of relational database like standardization, expressivity, provenance and supports SPARQL. Therefore, it helps to overcome the heterogeneity, thereby enabling the semantic interoperability in IoT.