This document describes Wise Store, a new model for organizing file metadata in large-scale distributed storage systems. Wise Store uses semantic grouping to organize metadata in a decentralized manner, constructing a semantic R-tree across storage units. This improves scalability and supports efficient composite queries like range, top-k, and search queries. Wise Store reduces query latency for these advanced metadata queries in systems with billions of files and exabytes of storage. It also enhances security using RSA encryption of metadata.