Can I choose to include only those miRNA gene targets that were validated by specific methods for network creation?

Yes, this task can be achieved using the Data Filter dialog on the Interaction Table page.

On the page, click the Data Filter button to bring up the dialog. On the list of methods, select those methods you want to include and click OK . The Interaction table will be filtered to contain only those validated by the selected approaches. Note, for organisms such as S.mansoni where only predicted interactions are available, you can select a threshold of the score to control the confidence level.