index.md

BioMedQuery Julia Package

Julia utilities to interact with BioMedical databases/APIs. Supported databases/APIS include:

National Library of Medicine (NLM)

• Entrez Programming Utilities (E-Utilities)
• Unified Medical Language System (UMLS)
• Clinical Trials (clinicaltrials.gov)

Installation

BioMedQuery is a registered package. To install the latest stable version, use the package manager.

Pkg.add("BioMedQuery")

Dependencies

###Registered Packages - automatically installed

• ArgParse
• SQLite
• MySQL
• Gumbo
• Requests
• DataStreams
• LightXML
• Requests
• HttpCommon
• BaseTestNext
• XMLconvert

Sister Packages

• PubMedMiner - Executables to search PubMed, link Mesh Descriptors to to UMLS concepts and visualize results.
• XMLConvert - Utilities to convert, flatten and explore XML file. Useful to investigate server responses.