Despite the rapidly growing applications of robots in industry, the use of robots to automate tasks in scientific laboratories is less prolific due to lack of generalized methodologies and high cost of hardware. This paper focuses on the automation of characterization tasks necessary for reducing cost while maintaining generalization, and proposes a software architecture for building robotic systems in scientific laboratory environment. A dual-layer (Socket.IO and ROS) action server design is the basic building block, which facilitates the implementation of a web-based front end for user-friendly operations and the use of ROS Behavior Tree for convenient task planning and execution. A robotic platform for automating mineral and material sample characterization is built upon the architecture, with an open source, low-cost three-axis computer numerical control gantry system serving as the main robot. A handheld laser induced breakdown spectroscopy (LIBS) analyzer is integrated with a 3D printed adapter, enabling automated 2D chemical mapping. We demonstrate the utility of automated chemical mapping by scanning of the surface of a spodumene-bearing pegmatite core sample with a 1071-point dense hyperspectral map acquired at a rate of 1520 bits per second. Automated LIBS scanning enables controlled chemical quantification in the laboratory that complements field-based measurements acquired with the same handheld device, linking resource exploration and processing steps in the supply chain for lithium-based battery materials.