We recognized recently that our approach to generating semantic phenotype data (e.g., see Balhoff et al. 2013 and Mikó et al. 2014) needed better documentation. Alas, here is the first draft of our manual, available through figshare:
Mikó I, Yoder MJ, Balhoff JP, Deans AR (2015): Generating semantic phenotypes. figshare. DOI: 10.6084/m9.figshare.1314904
We wrote it using Overleaf, which, I have to say, is pretty awesome.