The alignment process takes available mappings and produces a set of stable merges (output/domain_ontology/merges.csv). The goal is to have the minimal number of nodes, from the minimal number of different sources (ontologies).

The alignment process is a sequence of steps, where in each step we attempt to merge nodes to a given ontology. This alignment order is produced by putting the seed ontology as first (this should have the most mappings and the desired hierarchy), and the rest of the ontologies according to the frequency of the nodes.

First we use the strongest mapping relation type group, equivalence, then database reference and the rest. For more details about the alignment process, please read the docs.