Hi!
> I want to use UMBEL to calculate similarity value between concepts. 
> So, I need a taxonomy of concepts.
Good
> I've used skos:broaderTransitive property to construct hierarchical 
> taxonomic between reference concepts.
> Unfortunately, I found that the constructed graph is not DAG (Direct 
> Acyclic Graph).
Yeah, there are cycles in the graph.
> What do you suggest to convert constructed graph into DAG ?
You would have to detect the cycles and to remove the broaderTransitive 
triple that creates that cycle.
> I found also that there are many relations that could be used to 
> construct concepts taxonomy (like rdfs:subClassOf, skos:broader ...), 
> what the better relation to consider ?
You should consider using skos:broader/narrower for that kind of work.
Hope it helps!
Thanks,
Fred