Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine.

Many data resources generate, process, store, or provide kidney related molecular, pathological, and clinical data. Reference ontologies offer an opportunity to support knowledge and data integration. The Kidney Precision Medicine Project (KPMP) team contributed to the representation and addition of 329 kidney phenotype terms to the Human Phenotype Ontology (HPO), and identified many subcategories of acute kidney injury (AKI) or chronic kidney disease (CKD). The Kidney Tissue Atlas Ontology (KTAO) imports and integrates kidney-related terms from existing ontologies (e.g., HPO, CL, and Uberon) and represents 259 kidney-related biomarkers. We also developed a precision medicine metadata ontology (PMMO) to integrate 50 variables from KPMP and CZ CellxGene data resources and applied PMMO for integrative kidney data analysis. The gene expression profiles of kidney gene biomarkers were specifically analyzed under healthy control or AKI/CKD disease statuses. This work demonstrates how ontology-based approaches support multi-domain data and knowledge integration in precision medicine.

Approaches to prioritising primary health research: a scoping review.

OBJECTIVE: To systematically identify and describe approaches to prioritise primary research topics in any health-related area. METHODS: We searched Medline and CINAHL databases and Google Scholar. Teams of two reviewers screened studies and extracted data in duplicate and independently. We synthesised the information across the included approaches by developing common categorisation of relevant concepts. RESULTS: Of 44 392 citations, 30 articles reporting on 25 approaches were included, addressing the following fields: health in general (n=9), clinical (n=10), health policy and systems (n=10), public health (n=6) and health service research (n=5) (10 addressed more than 1 field). The approaches proposed the following aspects to be addressed in the prioritisation process: situation analysis/ environmental scan, methods for generation of initial list of topics, use of prioritisation criteria, stakeholder engagement, ranking process/technique, dissemination and implementation, revision and appeal mechanism, and monitoring and evaluation. Twenty-two approaches proposed involving stakeholders in the priority setting process. The most commonly proposed stakeholder category was 'researchers/academia' (n=17, 77%) followed by 'healthcare providers' (n=16, 73%). Fifteen of the approaches proposed a list of criteria for determining research priorities. We developed a common framework of 28 prioritisation criteria clustered into nine domains. The criterion most frequently mentioned by the identified approaches was 'health burden' (n=12, 80%), followed by 'availability of resources' (n=11, 73%). CONCLUSION: We identified and described 25 prioritisation approaches for primary research topics in any health-related area. Findings highlight the need for greater participation of potential users (eg, policy-makers and the general public) and incorporation of equity as part of the prioritisation process. Findings can guide the work of researchers, policy-makers and funders seeking to conduct or fund primary health research. More importantly, the findings should be used to enhance a more coordinated approach to prioritising health research to inform decision making at all levels.

A systematic review on the current status of adult diagnostic reference levels in head, chest and abdominopelvic Computed Tomography.

Computed tomography (CT) is a routinely employed diagnostic tool for the detection and diagnosis of disease processes. Despite the primary focus of radiation dose reduction and improvements in CT scanners, radiation dose exposure remains an ever-increasing concern. Scanning protocol optimisation relative to body weight and scanner manufacturer still lags behind the diagnostic reference levels (DRLs) that are set on an international scale. The aim of this systematic review is to evaluate the current status of adult DRLs in head, chest and abdominopelvic CT over time on a global scale. A search was carried out in early 2019 using the Medline, PubMed, EMBASE, SCOPUS and manual databases. The reference lists of published articles were also assessed to identify further articles. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) methodology was employed to evaluate articles for relevance. Articles were included if they assessed the DRL in head, chest and abdominopelvic scans. The search resulted in 6079 articles, of which 67 were included after a thorough screening process. The literature demonstrates a wide dose variation in reported head, chest and abdominopelvic dose length product (DLP) DRL, ranging from 700-1359, 330-707 and 550-1486 mGy·cm, respectively. Where reported, the volumed CT dose index (CTDIvol) DRL in the head, chest and abdominopelvic studies ranged from 30.4-85.5, 9-15 and 12.3-31 mGy·cm, respectively. The global means were shown to be slightly lower and significantly lower than the reported values of DLP and CTDIvol values for the American College of Radiology and European Commission, respectively. This review emphasises the need for an international standardisation for head and body DRL establishment methods, to provide a more comparable global measurement of dose variations across CT sites as well as regular monitoring of delivered radiation dose to patients.