Mathieu D'AQuin

Objective: Collaborate, Analyse, Research and Audit (CARA) project set out to provide an infrastructure to enable Irish general practitioners (GPs) to use their routinely collected patient management software (PMS) data to better understand their patient population, disease management and prescribing through data dashboards. This paper explains the design and development of the CARA infrastructure. Methods: The first exemplar dashboard was developed with GPs and focused on antibiotic prescribing to develop and showcase the proposed infrastructure. The data integration process involved extracting, loading and transforming de-identified patient data into data models which connect to the interactive dashboards for GPs to visualise, compare and audit their data. Results: The architecture of the CARA infrastructure includes two main sections: extract, load and transform process (ELT, de-identified patient data into data models) and a Representational State Transfer Application Programming Interface (REST API) (which provides the security barrier between the data models and their visualisation on the CARA dashboard). CARAconnect was created to facilitate the extraction and de-identification of patient data from the practice database. Discussion: The CARA infrastructure allows seamless connectivity with and compatibility with the main PMS in Irish general practice and provides a reproducible template to access and visualise patient data. CARA includes two dashboards, a practice overview and a topic-specific dashboard (example focused on antibiotic prescribing), which includes an audit tool, filters (within practice) and between-practice comparisons. Conclusion: CARA supports evidence-based decision-making by providing GPs with valuable insights through interactive data dashboards to optimise patient care, identify potential areas for improvement and benchmark their performance against other practices. Supplementary file 1. Graphical abstract

Building taxonomies is often a significant part of building an ontology, and many attempts have been made to automate the creation of such taxonomies from relevant data. The idea in such approaches is either that relevant definitions of the intension of concepts can be extracted as patterns in the data (e.g. in formal concept analysis) or that their extension can be built from grouping data objects based on similarity (clustering). In both cases, the process leads to an automatically constructed structure, which can either be too coarse and lacking in definition, or too fined-grained and detailed, therefore requiring to be refined into the desired taxonomy. In this paper, we explore a method that takes inspiration from both approaches in an iterative and interactive process, so that refinement and definition of the concepts in the taxonomy occur at the time of identifying those concepts in the data. We show that this method is applicable on a variety of data sources and leads to taxonomies that can be more directly integrated into ontologies.

Building taxonomies is often a significant part of building an ontology, and many attempts have been made to automate the creation of such taxonomies from relevant data. The idea in such approaches is either that relevant definitions of the intension of concepts can be extracted as patterns in the data (e.g. in formal concept analysis) or that their extension can be built from grouping data objects based on similarity (clustering). In both cases, the process leads to an automatically constructed structure, which can either be too coarse and lacking in definition, or too fined-grained and detailed, therefore requiring to be refined into the desired taxonomy. In this paper, we explore a method that takes inspiration from both approaches in an iterative and interactive process, so that refinement and definition of the concepts in the taxonomy occur at the time of identifying those concepts in the data. We show that this method is applicable on a variety of data sources and leads to taxonomies that can be more directly integrated into ontologies.

The tonal centre of a piece of music is crucial for perception and understanding, estimating the root note is an important issue in music information retrieval. To determine the root note of a melody, previously published methods generally involve matching the histogram of pitch classes in the melody with pre-calculated pitch class profiles. Performance varies between methods depending on these profiles, as there is no universally agreed-upon set of profiles. Furthermore, these methods do not consider structural information. In this study, we present an ensemble machine learning-based algorithm for root note prediction. In the proposed methodology, we estimate the key of a piece using several existing pitch-class profile algorithms and several simple key-estimation heuristics. We then feed these results into a machine-learning model. Experiments are conducted on the Ceol Rince na hEireann dataset, which contains 1,224 Irish traditional dance music melodies. The dataset is unbalanced, with some possible root notes occurring rarely or never, reflecting common practice in the tradition. To achieve a balanced dataset, we employed both simple oversampling and the Synthetic Minority Over-sampling Technique (SMOTE). The experiments revealed that the Random Forest classifier, trained on a balanced dataset, performed the best. The F1 score was approximately 0.90 when tested on unseen data.

The open science movement has gained significant momentum within the last few years. This comes along with the need to store and share research artefacts, such as publications and research data. For this purpose, research repositories need to be established. A variety of solutions exist for implementing such repositories, covering diverse features, ranging from custom depositing workflows to social media-like functions.In this article, we introduce the FAIREST principles, a framework inspired by the well-known FAIR principles, but designed to provide a set of metrics for assessing and selecting solutions for creating digital repositories for research artefacts. The goal is to support decision makers in choosing such a solution when planning for a repository, especially at an institutional level. The metrics included are therefore based on two pillars: (1) an analysis of established features and functionalities, drawn from existing dedicated, general purpose and commonly used solutions, and (2) a literature review on general requirements for digital repositories for research artefacts and related systems. We further describe an assessment of 11 widespread solutions, with the goal to provide an overview of the current landscape of research data repository solutions, identifying gaps and research challenges to be addressed.