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POGraph database (neo4j) vs relational database. Need help in design
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copied!<p>I have to work with an open source project (<a href="http://biojava.org/wiki/Main_Page" rel="nofollow">biojava</a>), but I'm not satisfied with some performance, and I'd like to spend some time to improve it.</p> <p>For example, I have a text database coded in this way:</p> <pre><code>chrX Cufflinks exon 65175856 65175971 . . . gene_id "XLOC_002576"; transcript_id "TCONS_00004217"; exon_number "1"; gene_name "RP6-159A1.2"; oId "CUFF.3698.1"; nearest_ref "ENST00000456392"; class_code "p"; tss_id "TSS3873"; chrX Cufflinks exon 128986006 128986088 . . . gene_id "XLOC_002577"; transcript_id "TCONS_00004218"; exon_number "1"; oId "CUFF.3750.1"; class_code "u"; tss_id "TSS3874"; </code></pre> <p>Not every field is mandatory, each <code>gene_id</code> may be associated to multiple <code>transcript_id</code> (1..n), and each <code>transcript_id</code> has 1 or more <code>exon</code>.</p> <p>The library behavior is to load the entire text file in an <code>ArrayList</code>, and for each search al the list must be iterated. This works good with small lists, but in my case I have 10^10 queries with a really large list, and it takes a couple of days in a good computer.</p> <p>Would Neo4j be a good choice? What would be a good way to implement it? For example, is it bad to create a String only entity, and make relationships between them? Or is it better to use Hsqldb with a single table?</p> <p>Please note I don't need persistence, but speed and synchronization is mandatory.</p> <p>EDIT: if you want, you can have a look at the project <a href="https://github.com/biojava/biojava/tree/master/biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff" rel="nofollow">here</a>. </p>

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