Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR.

In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of (meta-) data in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. VCF files are an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant call data (for example, the HapMap format and the gVCF format), but none currently have the reach of VCF. In VCF, only the sites of variation are described, whereas in gVCF, all positions are listed, and confidence values are also provided. For the sake of simplicity, we will only discuss VCF and our recommendations for its use. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse (if any) descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from the plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.

ELIXIR biovalidator for semantic validation of life science metadata.

SUMMARY: To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents. AVAILABILITY AND IMPLEMENTATION: Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BioSamples database: FAIRer samples metadata to accelerate research data management.

The BioSamples database at EMBL-EBI is the central institutional repository for sample metadata storage and connection to EMBL-EBI archives and other resources. The technical improvements to our infrastructure described in our last update have enabled us to scale and accommodate an increasing number of communities, resulting in a higher number of submissions and more heterogeneous data. The BioSamples database now has a valuable set of features and processes to improve data quality in BioSamples, and in particular enriching metadata content and following FAIR principles. In this manuscript, we describe how BioSamples in 2021 handles requirements from our community of users through exemplar use cases: increased findability of samples and improved data management practices support the goals of the ReSOLUTE project, how the plant community benefits from being able to link genotypic to phenotypic information, and we highlight how cumulatively those improvements contribute to more complex multi-omics data integration supporting COVID-19 research. Finally, we present underlying technical features used as pillars throughout those use cases and how they are reused for expanded engagement with communities such as FAIRplus and the Global Alliance for Genomics and Health. Availability: The BioSamples database is freely available at http://www.ebi.ac.uk/biosamples. Content is distributed under the EMBL-EBI Terms of Use available at https://www.ebi.ac.uk/about/terms-of-use. The BioSamples code is available at https://github.com/EBIBioSamples/biosamples-v4 and distributed under the Apache 2.0 license.

The quality of outpatient primary care in public and private sectors in Sri Lanka--how well do patient perceptions match reality and what are the implications?

OBJECTIVE: To compare the quality of clinical care and patient satisfaction in public and private outpatient primary care services in Sri Lanka. METHODS: A prospective, cross-sectional comparison was done by direct observation of patient encounters and exit interviews of outpatients in 10 public hospital general outpatient clinics and 66 private practitioner clinics in three districts of Sri Lanka. A total of 1027 public sector patients and 944 private sector patients were surveyed. Data were collected for 39 quality indicators covering diarrhoea, cough, hypertension, diabetes, asthma, upper respiratory tract infections (URTI) and five other conditions, along with prescribing indicators. The exit interviews collected data for 10 patient satisfaction indicators. RESULTS: The public sector performed better for some conditions (diarrhoea, cough and asthma) and the private sector performed better for others (hypertension, diabetes, URTI and tonsillitis). Overall quality was similar between the sectors in the domains of history taking, examination and investigations and management, but the private sector performed much better on patient education (57 vs 12%). Overall patient satisfaction was high in both sectors (98%), although the private sector performed much better in interpersonal satisfaction (94 vs 84%) and system-related indicators (95 vs 84%). Comparisons with studies from other countries suggest that both sectors perform considerably better than India, and similarly in many indicators to high-income countries. CONCLUSIONS: Quality of outpatient primary care in Sri Lanka is generally high for a lower-middle income developing country. The public and private sectors perform similarly, except that private sector patients have longer consultations, are more likely to receive education and advice, and obtain better interpersonal satisfaction. The public system, with its limited funding, is able to deliver care in diagnosis and management that is similar to the private sector, while private sector patients, who spend more on their healthcare receive better quality care in non-clinical areas.