CSpace is a concise word embedding of bio-medical concepts that outperforms all alternatives in terms of out-of-vocabulary ratio (OOV) and semantic textual similarity (STS) task and have comparable performance with respect to transformer-based alternatives in the sentence similarity task. CSpace also encodes ontological IDs (MeSH, NCBI gene and tax ID) and can be used for measuring the relatedness of diseases, genes or conditions, potentially unlocking previously unknown disease-condition association, as well as for semantic synonyms search. The code used for data pre-processing, training and evaluation of CSpace, all the experiments results and test benchmarks are available in the GitHub repository https://github.com/cosbi-research/cspace