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bioRxiv · 10.1101/2023.05.09.539725

NGBO: Introducing -omics metadata to biobanking ontology.

Alghamdi, D.·Dooley, D.·Samman, M.·Hsiao, W.
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Abstract

BackgroundWith improvements in high throughput sequencing technologies and the constant generation of large biomedical datasets, biobanks increasingly take on the role of managing and delivering not just specimens but also data. However, re-using data from different biobanks is challenged by incompatible data representations. Contextual data describing biobank digital resources often contain unstructured textual information incompatible with computational processes such as automated data discovery and integration. Therefore, a consistent and comprehensive contextual data framework is needed to increase discovery, reusability, and integrability across data sources. MethodsBased on available genomics standards (e.g., Minimum information about a microarray experiment (MIAME)), the College of American Pathologists (CAP) laboratory accreditation requirements, and the Open Biological and Biomedical Ontologies Foundry principles, we developed the Next Generation Biobanking Ontology (NGBO). In addition, we created new terms and re-used concepts from the Ontology for Biomedical Investigations (OBI) and the Ontology for Biobanking (OBIB) to build NGBO. ResultsThe Next Generation Biobanking Ontology https://www.ebi.ac.uk/ols4/ontologies/ngbo is an open application ontology representing omics contextual data, licensed under the Apache License 2.0. The ontology focuses on capturing information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to process and interpret data, and data management. In this paper, we demonstrated the use of the NGBO to add semantic statements to real-life use cases and query data previously stored in unstructured textual format.

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Alghamdi, D., Dooley, D., Samman, M., Hsiao, W.. 2023-05-10. NGBO: Introducing -omics metadata to biobanking ontology.. https://doi.org/10.1101/2023.05.09.539725

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