SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

Abstract Summary To unlock the full potential of genome data and to enhance data interoperability and reusability of genome annotations we have developed SAPP, a Semantic Annotation Platform with Provenance. SAPP is designed as an infrastructure supporting FAIR de novo computational genomics but can also be used to process and analyze existing genome annotations. SAPP automatically predicts, tracks and stores structural and functional annotations and associated dataset- and element-wise provenance in a Linked Data format, thereby enabling information mining and retrieval with Semantic Web technologies. This greatly reduces the administrative burden of handling multiple analysis tools and versions thereof and facilitates multi-level large scale comparative analysis. Availability and implementation SAPP is written in JAVA and freely available at https://gitlab.com/sapp and runs on Unix-like operating systems. The documentation, examples and a tutorial are available at https://sapp.gitlab.io.