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. 2016 Jan 16;10:4. doi: 10.1186/s40246-016-0061-7

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© Patterson et al. 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — Flow of data through the clinical pipeline. Patient sample sequence data from the clinical genome analytics (CGA) pipeline is integrated with sample meta-data from the Laboratory Information Management System (LIMS), and called variants are mapped to the JAX-Clinical Knowledgebase (JAX-CKB) database. The JAX-CKB incorporates information populated from various incorporated ontologies and databases, and via the curation User Interface (UI), and is maintained using the CKB-Utilities tools. Using information from the JAX-CGA/CKB and the CKB reports, tools are used to generate datasets to enable clinical report generation