A novel metadata management model to capture consent for record linkage in longitudinal research studies

McMahon, Christiana; Denaxas, Spiros

doi:10.1080/17538157.2017.1364251

Cited by 1 publication

(1 citation statement)

References 63 publications

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“…For example, the U.S. interagency One Health Enteric Package may be more readily compared with the One Health AMR standard being developed by a joint-agency Canadian initiative [37]. Complete and consistent metadata enhances the efficiency of epidemiological investigations, as evidenced by other groups who have successfully applied ontology-based approaches including NCBI and EMBL-EBI [27,38]. However, to our knowledge, this is the first schema that has been developed to capture machine-readable descriptions of swab site locations in built environments, building on the MixS minimum metadata standard from for built environments [7].…”

Section: Resultsmentioning

confidence: 99%

A schema for digitized surface swab site metadata in open-source DNA sequence databases

Feng

Daeschel

Dooley³

et al. 2022

Preprint

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Large, open-source DNA sequence databases have been generated, in part, through the collection of microbial pathogens from swabbing surfaces in built environments. Analyzing these data in aggregate through public health surveillance requires digitization of the complex, domain-specific metadata associated with swab site locations. However, the swab site location information is currently collected in a single, free-text ISOLATION SOURCE field promoting generation of poorly detailed descriptions with varying word order, granularity, and linguistic errors, making automation difficult and reducing machine-actionability. We assessed 1,498 free-text swab site descriptions generated during routine foodborne pathogen surveillance. The lexicon of free-text metadata was evaluated to determine the informational facets and quantity of unique terms used by data collectors. Open Biological Ontologies (OBO) foundry libraries were used to develop hierarchical vocabularies connected with logical relationships to describe swab site locations. Five informational facets described by 338 unique terms were identified via content analysis. Term hierarchy facets were developed as were statements (called axioms) about how entities within these five domains were related. The schema developed through this study has been integrated into a publicly available pathogen metadata standard, facilitating ongoing surveillance and investigations. The One Health Enteric Package is available at NCBI BioSample beginning in 2022. Collective use of metadata standards increases the interoperability of DNA sequence databases, enabling large-scale approaches to data sharing, artificial intelligence, and big-data solutions to food safety.

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Section: Resultsmentioning

confidence: 99%