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 […]

Excel mangles NCBI gene symbols

Using Microsoft’s Excel for bioinformatics work sucks, but sometimes a spreadsheet is the best format for communicating results to other scientists. The program’s default behavior mangles some NCBI gene symbols when you import them from a text file. Here is how to deal with it. Suppose you have the following list of gene symbols, and […]