Cross-organism analysis using InterMine.
Document Type
Article
Publication Date
8-1-2015
Keywords
Animals, Computational Biology, Databases, Factual, Databases, Genetic, Genomics, Humans, Internet, Software, Systems Integration, User-Computer Interface
JAX Source
Genesis 2015 Aug; 53(8):547-60.
Volume
53
Issue
8
First Page
547
Last Page
560
ISSN
1526-968X
PMID
26097192
DOI
https://doi.org/10.1002/dvg.22869
Abstract
InterMine is a data integration warehouse and analysis software system developed for large and complex biological data sets. Designed for integrative analysis, it can be accessed through a user-friendly web interface. For bioinformaticians, extensive web services as well as programming interfaces for most common scripting languages support access to all features. The web interface includes a useful identifier look-up system, and both simple and sophisticated search options. Interactive results tables enable exploration, and data can be filtered, summarized, and browsed. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other entities. InterMine databases have been developed for the major model organisms, budding yeast, nematode worm, fruit fly, zebrafish, mouse, and rat together with a newly developed human database. Here, we describe how this has facilitated interoperation and development of cross-organism analysis tools and reports. InterMine as a data exploration and analysis tool is also described. All the InterMine-based systems described in this article are resources freely available to the scientific community.
Recommended Citation
Lyne R,
Sullivan J,
Butano D,
Contrino S,
Heimbach J,
Hu F,
Kalderimis A,
Lyne M,
Smith R,
Štěpán R,
Balakrishnan R,
Binkley G,
Harris T,
Karra K,
Moxon S,
Neuhauser S,
Ruzicka L,
Cherry M,
Richardson J,
Stein L,
Westerfield M,
Worthey E,
Micklem G.
Cross-organism analysis using InterMine. Genesis 2015 Aug; 53(8):547-60.