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. 2024 Sep 3;30(12):3578–3589. doi: 10.1038/s41591-024-03239-5

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

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Extended Data Fig. 1 — (A) Indexing in Domain view is done by clinical table and then OMOP vocabulary hierarchy. Each clinical domain has its own exclusive set of streams. Concepts are grouped by ancestor concept using the vocabulary hierarchy. Each ancestor group gets its own stream. Indexing in Person view is by person (person ID). All data (clinical or genetic) for a patient are inserted into the same stream. For clinical this is irrespective of domain and for variant this is irrespective of genomic coordinate bin. Note within a single stream, multiple patient data can be inserted. Indexing in Variant/Gene view is by genomic coordinate bin. All variants/genes within a set of continuous genomic coordinates are added to a single stream. Indexing in Analysis is by analysis type. Data for kinship and population stratification is stored per sample and data for sequencing metadata is stored by metadata type. (B) Flowchart of query process. User inputs required fields into the query module. The mapping stream is searched for the location of the stream holding data for that concept ID. The stream location is extracted from the mapping stream and the concept ID is searched in that stream. Person IDs returned from the stream search are retrieved and processed into a table. If additional search filters are added, these are processed on the returned data.