Due to the increasing adoption of electronic health records (EHR), large scale EHRs have become another rich data source for translational clinical research. Despite its potential, deriving generalizable knowledge from EHR data remains challenging. First, EHR data are generated as part of clinical care with data elements too detailed and fragmented for research. Despite recent progress in mapping EHR data to common ontology with hierarchical structures, much development is still needed to enable automatic grouping of local EHR codes to meaningful clinical concepts at a large scale. Second, the total number of unique EHR features is large, imposing methodological challenges to derive reproducible knowledge graph, especially when interest lies in conditional dependency structure. Third, the detailed EHR data on a very large patient cohort imposes additional computational challenge to deriving a knowledge network. To overcome these challenges, we propose to infer the conditional dependency structure among EHR features via a latent graphical block model (LGBM). The LGBM has a two layer structure with the first providing semantic embedding vector (SEV) representation for the EHR features and the second overlaying a graphical block model on the latent SEVs. The block structures on the graphical model also allows us to cluster synonymous features in EHR. We propose to learn the LGBM efficiently, in both statistical and computational sense, based on the empirical point mutual information matrix. We establish the statistical rates of the proposed estimators and show the perfect recovery of the block structure. Numerical results from simulation studies and real EHR data analyses suggest that the proposed LGBM estimator performs well in finite sample.