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View article: Semantic Representation of Medical Data Collection Forms Using Standards
Semantic Representation of Medical Data Collection Forms Using Standards Open
Data collection forms and questionnaires are widely used to capture patient data, but their development often receives insufficient attention. The RES-Q+ project aims to semantically standardise a widely used international stroke registry …
View article: ‘SNOMEDizing’ Questionnaires for Standardizing Stroke Registry Data
‘SNOMEDizing’ Questionnaires for Standardizing Stroke Registry Data Open
International interoperability of healthcare and research data requires a commitment to standards. To this end, SNOMED CT was evaluated for representing questionnaire items of the European Registry of Stroke Care Quality using a complex an…
View article: A knowledge graph-based data harmonization framework for secondary data reuse
A knowledge graph-based data harmonization framework for secondary data reuse Open
The flexible data representation using RDF, together with the formal semantic underpinning provided by the SCDM, have enabled the semantic integration, query and advanced exploitation of heterogeneous data in the context of the Precise4Q p…
View article: Improving the Quality and Utility of Electronic Health Record Data through Ontologies
Improving the Quality and Utility of Electronic Health Record Data through Ontologies Open
The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many…
View article: SNOMED CT and Basic Formal Ontology – convergence or contradiction between standards? The case of “clinical finding”
SNOMED CT and Basic Formal Ontology – convergence or contradiction between standards? The case of “clinical finding” Open
Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an o…
View article: Supporting SNOMED CT postcoordination with knowledge graph embeddings
Supporting SNOMED CT postcoordination with knowledge graph embeddings Open
SNOMED CT postcoordination is an underused mechanism that can help to implement advanced systems for the automatic extraction and encoding of clinical information from text. It allows defining non-existing SNOMED CT concepts by their relat…
View article: HURON: A Quantitative Framework for Assessing Human Readability in Ontologies
HURON: A Quantitative Framework for Assessing Human Readability in Ontologies Open
The increasing use of ontologies requires their quality assurance. Ontology quality assurance consists of a set of activities that allow analyzing the ontology, identifying strengths and weaknesses, and proposing improvement actions. Human…
View article: Few-Shot Cross-lingual Transfer for Coarse-grained De-identification of Code-Mixed Clinical Texts
Few-Shot Cross-lingual Transfer for Coarse-grained De-identification of Code-Mixed Clinical Texts Open
Despite the advances in digital healthcare systems offering curated structured knowledge, much of the critical information still lies in large volumes of unlabeled and unstructured clinical texts. These texts, which often contain protected…
View article: Digital twins and hybrid modelling for simulation of physiological variables and stroke risk
Digital twins and hybrid modelling for simulation of physiological variables and stroke risk Open
One of the more interesting ideas for achieving personalized, preventive, and participatory medicine is the concept of a digital twin. A digital twin is a personalized computer model of a patient. So far, digital twins have been constructe…
View article: Few-Shot Cross-lingual Transfer for Coarse-grained De-identification of Code-Mixed Clinical Texts
Few-Shot Cross-lingual Transfer for Coarse-grained De-identification of Code-Mixed Clinical Texts Open
Despite the advances in digital healthcare systems offering curated structured knowledge, much of the critical information still lies in large volumes of unlabeled and unstructured clinical texts. These texts, which often contain protected…
View article: FastText embeddings obtained from SNOMED CT - Spanish and International
FastText embeddings obtained from SNOMED CT - Spanish and International Open
FastText model trained in a corpus that was obtained from SNOMED CT by performing random walks. There are three models: one trained using all relations available in the international version of SNOMED CT, another one trained using only is_…
View article: FastText embeddings obtained from SNOMED CT - Spanish and International
FastText embeddings obtained from SNOMED CT - Spanish and International Open
FastText model trained in a corpus that was obtained from SNOMED CT by performing random walks. There are three models: one trained using all relations available in the international version of SNOMED CT, another one trained using only is_…
View article: Towards a Semantic Data Harmonization Federated Infrastructure
Towards a Semantic Data Harmonization Federated Infrastructure Open
Data integration is an increasing need in medical informatics projects like the EU Precise4Q project, in which multidisciplinary semantically and syntactically heterogeneous data across several institutions needs to be integrated. Besides,…
View article: Semankey: A Semantics-Driven Approach for Querying RDF Repositories Using Keywords
Semankey: A Semantics-Driven Approach for Querying RDF Repositories Using Keywords Open
The Web of Data aims at linking Internet data repositories. Semantic Web technologies make data easily readable by computer agents, enabling the automation of complex tasks and facilitating data integration. They facilitate the achievement…
View article: Clinical Text Mining on FHIR
Clinical Text Mining on FHIR Open
Semantic standards and human language technologies are key enablers for semantic interoperability across heterogeneous document and data collections in clinical information systems. Data provenance is awarded increasing attention, and it i…
View article: Qualitative analysis of manual annotations of clinical text with SNOMED CT
Qualitative analysis of manual annotations of clinical text with SNOMED CT Open
SNOMED CT provides about 300,000 codes with fine-grained concept definitions to support interoperability of health data. Coding clinical texts with medical terminologies it is not a trivial task and is prone to disagreements between coders…
View article: Semantic enrichment of clinical models towards semantic interoperability. The heart failure summary use case
Semantic enrichment of clinical models towards semantic interoperability. The heart failure summary use case Open
Objective To improve semantic interoperability of electronic health records (EHRs) by ontology-based mediation across syntactically heterogeneous representations of the same or similar clinical information. Materials and Methods Our approa…