Which is the best way to index the data from relational database

Elastic Stack Elasticsearch
2

My advice:

Think about the use case, not the current implementation.
Basically ask yourself: "What type of data my user will be searching for?".

As an example, let's say that users want to search for employees. Then index employees.

2nd question is "What kind of attributes do my users will use to search?". Let's say "company name", "company website" and "employee name". Then just store those values within each document, like:

PUT employees/_doc/david
{
  "name": "David XYZ",
  "company": {
    "name": "elastic",
    "website": "https://elastic.co"
  }
}

So don't try to reimplement relational model if it's not absolutely needed but just focus first on the use case.

For the record I shared most of my thoughts there: http://david.pilato.fr/blog/2015/05/09/advanced-search-for-your-legacy-application/