semantic similarity measurement for cell line ontologies
About the metric you use, there are several reviews on the topic, if I recall well I think that the information content based are the best ones, of those, I only recognized the JiangConrathSemSim listed on the webpage. 

However, if you want to use a semantic similarity measure I would use the BMA method, which is more comprehensive than other methods. But the BMA method is only a way to aggregate several metrics of ontologies into a single numeric value. I am not confident that FastSemSim implements correctly those methods.

Note, that according to the license, you should contact the authors before using it:


  You must contact us before using it or its results or any application/tool based on it in any published work.




I am not sure that the cell lines fit in a ontolgogy. Because ontologies are defined as directed acyclic graph (DAG) and there are some cycles that happens in cells like the induced pluripotent stem cells show. However they might be right if you just compare the cell lines and not the state of the cells on those lines (use it only if you want to compare the lineage of your cells lines).