This document describes the development and definition of a set of vendor-neutral protocols and APIs necessary to build the full Science Mesh service, including federated sharing of data, access to application functionality and infrastructure integration. Our approach is based on: maturing and extending protocols already in use by CS3 community (e.g. OCM, CS3APIs) with the aim to advance these protocols from TRL6 to TRL9; adopting other existing standard protocols wherever appropriate (e.g. WOPI, WebDAV,...). This document is divided in several sections. Core APIs identifies the core APIs and protocols for the Science Mesh service: OCM and CS3APIs. Use Cases further explores the usage of these interfaces in the four reference application workflows developed in the context of Work Package 4: Data Science Environments, Open Data Systems, Collaborative Document Editing and On-Demand Data Transfers. EFSS integration with IOP section describes the architecture connecting EFSS with the Interoperability Platform (IOP). IOP provides the reference implementation for the Core and Use-Case APIs. Integration of Peer-to-Peer architecture with IOP is described based on the Cubbit implementation. ScienceMesh Infrastructure APIs are presented for monitoring endpoints.