Revised solr document loader codes to deep-copy all relevant ontologies

[yy20716]

This patch is for resolving the issue, i.e. the previous codes did not deep-copy all relevant ontologies in the manager, which leads to producing incorrect label and missing biological processes in solr index entries.

@kltm Seth, if you don't mind, could you please test generating the solr index using this version? Thank you for your time.