Stem cells are arguably one of the original synthetic cells used in mammalian research. Although originally isolated from human cultured blastocysts, the identity of a human embryonic stem cell with respect to any genuine developmental equivalent remains highly controversial. More recent technological advances in stem cell biology allows the reprogramming of any mature cell back to a stem-like state. In this talk I will describe the Stemformatics stem cell atlas, which has collated the largest body of molecular phenotyping of human stem cells. Stemformatics is designed for non experts to explore stem cell transcriptome, proteome and epigenome datasets. I will discuss the discovery of new classes of pluripotent stem cells using the Stemformatics resource.