Data publication for the paper "Fabrication uncertainty guided design optimization of a photonic crystal cavity by using Gaussian processes" Contains scripts for performing fabrication uncertainty guided design optimization, example scripts, research data (raw data), cleanup), additional information on models, convergence plots, and field exports. Funding We acknowledge funding by the German Federal Ministry of Education and Research (BMBF project siMLopt number 05M20ZAA and BMBF Forschungscampus MODAL number 05M20ZBM) as well as funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy -- The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). This project (20FUN05 SEQUME) has received funding from the EMPIR programme co-financed by the Participating States and from the European Union’s Horizon 2020 research and innovation programme. This project is co-financed by the European Regional Development Fund (EFRD, application no. 10184206, QD-Sense).