I am trying to create one knowledge base (single source of truth) gathered from multiple web sources. (ex. wiki <-> fandom)
So I want to try a Siamese network or calculate cosine similarity with BERT embedded documents.
Then, can I ignore those json structures and train them anyway?
Although BERT wasn't specifically trained to find similarity between JSON data, you could always extract and concatenate the values of your JSON into a long sentence and leave it to BERT to capture the context as you expect.
Alternatively, you could generate a cosine similarity score for each key-value dependency between the JSONs and aggregate them to generate a net similarity score for the JSON data pair.
Also, see Sentence-BERT (SBERT), a modification of the pre-trained BERT network that use siamese and triplet network structures to derive semantically meaningful sentence embeddings that can be compared using cosine-similarity.