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Permalink Reply by Juan Rolando Reza on March 16, 2015 at 4:45pm

Database representation of graph-structured information is fascinating in its own right.

I have been studying genomics technology in which graphs play a big role, both as information-structure that is the basis of certain algorithms, as well as the data driving visualizations or visually-interesting real-world structures.

As an example, here is a visualization of a protein complex that catches the eye.

See http://en.wikipedia.org/wiki/FOXP2#/media/File:Protein_FOXP2_PDB_2a...

The image is a Richardson diagram which is (mostly) automatically generated from a database describing the molecular structure of the protein. This type of diagram was invented (i.e. originally hand-drawn) by Jane Richardson, PhD.

I wonder if the book "Graph Databases" touches on this.

Presently, I am doing a research study on a particular feature of the epigenome. It involves large DNA databases (actually, structured flat files), elaborate algorithms for sequence correlation, and histone complexes. Each of these involves graph-theoretic representations and inference functions from graph structures.

The "databases" I know for DNA, the transcriptome, pathways, etc. do not lend themselves to conventional SQL, or even noSQL as far as I know to date. (Chime in anyone? )

I will be presenting a paper at the IEEE SouthCon conference in April 2015 which touches on a graph-theoretic feature of certain (sequencing) problems lending itself to massively-parallel-ization of linearly-expressable algorithms.

I am pleased to see a free book on graph databases. Thanks!