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Using Semantic Technologies to Enhance Metadata Submissions to Public Repositories in Biomedicine

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journal contribution
posted on 04.12.2018, 08:33 by Attila L. Egyedi, Martin J. O’Connor, Marcos Martínez-Romero, Debra Willrett, Josef Hardi, John Graybeal, Mark A. Musen

The emergence of the FAIR principles is driving renewed efforts in the biomedical community to produce high-quality metadata that describe da- tasets submitted to public repositories. A variety of organizations are now in- volved in developing submission pipelines that place a strong emphasis on ac- companying submissions with highly descriptive metadata. However, these pipe- lines have highly variable requirements, which range from using ontology-based metadata in existing submission pipelines to supporting end-to-end metadata management in new pipelines. There is a lack of tools for integrating metadata support when building these pipelines. In this paper we describe a system called CEDAR that aims to address this challenge. The described tools provide a flexi- ble, highly configurable solution for producing submission workflows with se- mantically rich metadata support. We outline how we have used these tools to deliver robust metadata submission pipelines for several communities, including the Adaptive Immune Receptor Repertoire (AIRR), the NIH Cloud Credits Model Pilot (CCP), and the Library of Integrated Network-based Cellular Signa- tures (LINCS).


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