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. 2018 Aug 16;9:1877. doi: 10.3389/fimmu.2018.01877

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Copyright © 2018 Bukhari, O’Connor, Martínez-Romero, Egyedi, Willrett, Graybeal, Musen, Rubelt, Cheung and Kleinstein.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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CAIRR Submission Pipeline Workflow. (1) The CEDAR Template Designer is employed to create a set of templates according to the Minimal Information about an Adaptive Immune Receptor Repertoire (MiAIRR) standard. (2) Scientists can log into the CEDAR Workbench and use these templates to edit ontology-controlled metadata associated with their AIRR-sequencing study. The edited metadata is pre-validated through the National Center for Biotechnology Information (NCBI) validation service. (3) Scientists can start the submission process by accessing the Submission Manager within their CEDAR Workbench workspace. (4) The Submission Manager connects the CEDAR Workbench to the NCBI. (5) The Submission Manager facilitates uploading the metadata and data (FASTQ files) to the NCBI. (6) The CAIRR pipeline periodically checks the submission status at the NCBI. (7) Alert messages from NCBI are received by the Submission Manager. (8) These alert messages provide step-by-step processing detail to the scientists.