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    <p>You need to build a master index that will store each triple and in how many files it appears and the exact file name and location of the triple within each file. You can search the master index to answer the queries in real-time.</p> <p>As you update, delete or create new rdf files, you need to update the master index.</p> <p>You need to store the master index so that it can be updated, searched efficiently.</p> <p>Simple choice could be to use relational database (like MySql) to store the master index. It can answer you queries like finding common triples with simple select statement <code>select * from rdfindex where triplecount &gt; 2.</code></p> <p><strong>EDIT:</strong> You cannot store hundreds of thousands of triples in memory using HashMap or similar datastructure. That's why I suggested using database, which can store the data and respond to your queries efficiently. You can look at embedded database like SQLite to store the data.</p> <p>Read upon these topics</p> <p><a href="https://stackoverflow.com/questions/8907645/beginner-in-sqlite">How to create SQLite database and create tables, access tables etc.,</a> Create a simple table to store triple, triplecount, filenames.</p> <p>Convert all your Excel files to CSV files. You can use <a href="http://opencsv.sourceforge.net/" rel="nofollow noreferrer">opencsv</a> to parse the file in Java (check out the samples that come with opencsv). </p> <p>Parse the CSV files and load the data into SQLite. If the triple is already in the database, then just update the count, if not insert the triple.</p>
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