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 […]

gene annotation database with MongoDB

After reading Datanami’s recent post “9 Must-Have Skills to Land Top Big Data Jobs in 2015” [1], I decided to round out my NoSQL knowledge by learning MongoDB. I have previously reported NoSQL work with Neo4j on this blog, where I discussed building a gene annotation graph database [2]. Here I build a similar gene […]

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 […]