bio2bel / hmdd

A Bio2BEL package for converting the Human microRNA Disease Database (HMDD) to BEL

Bio2BEL HMDD

Converts the Human microRNA Disease Database to BEL

Citation

Li Y, Qiu C, Tu J, et al. HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Research. 2014;42(Database issue):D1070-D1074. doi:10.1093/nar/gkt1023.

Abstract

HMDD (the Human microRNA Disease Database) is a database that curated experiment-supported evidence for human microRNA (miRNA) and disease associations. miRNAs are one class of important regulatory RNAs, which mainly repress gene express at the post-transcriptional level. Increasing reports have shown that miRNAs play important roles in various critical biological processes. For their importance, the dysfunctions of miRNAs are associated with a broad spectrum of diseases. The first version of HMDD was built on December 2007. Each entry in HMDD v1.0 has four items for annotation; they are miRNA name, disease name, the reference PubMed ID, and the evidence supporting the miRNA-association from the original paper. During the past five years, we updated HMDD for more than 30 times. HMDD v2.0 presents more detailed and comprehensive annotations to the human miRNA-disease association data, including miRNA-disease association data from the evidence of genetics, epigenetics, circulating miRNAs, and miRNA-target interactions. In addition, a “submission” function was implemented in the version 2.

Links

• Database: http://www.cuilab.cn/hmdd
• Data: http://www.cuilab.cn/files/images/hmdd2/alldata.txt

hmdd's Issues

Create testing suite

• Take a small slice of the full testing file specified in the README
• Tests for database population
• Tests for BEL graph enrichment