a graph-based, large-scale data model for NLP cross-referencing

I find myself in a situation where my team needs to combine several natural language processing (NLP) [1] techniques, each conducted upon the same large set of texts, to derive critical business conclusions. Particularly, we need a way to cross-reference analyses based on common key words across sentences. Toward that end, I designed the following […]

graph database for heterogeneous biological data

To assist with a project I’m working on, I recently implemented a substantial portion of DisGeNET as a graph database. Furthermore, I added MeSH, OMIM, Entrez, and GO into the database to facilitate linking of data between these sources. Here I briefly describe these data sources, describe graph databases, and then show how use of […]

graph database for gene annotation

Lately I’ve been experimenting with graph databases using Neo4j and the Cypher query language. To get a feel for these tools, I created the following gene annotation network. The Cypher commands I used are discussed in this post, followed by a demonstration of querying the database. Creating the Graph Database We are creating the following […]