Analysis and Visualisation
Significant progress has been made over the last decade in organizing and categorizing our scientific knowledge with some of the major discoveries of the late 20th and early 21st century maturing into every-day methods (mass spectrometry, whole-genome sequencing, microarrays, protein arrays, lipid arrays).
The now systematized resources at EMBL-EBI, GO, as well as online databases such as HPRD, UniProt, Reactome and hundreds more provide access to data categorized by nearly any feature of interest from molecule-specific, through interactions, structure, up to function. Most provide at least rudimentary access through their websites, the largest ones allowing API access and data download, and many having expanded to become key points for every biologist’s routine research (e.g. KEGG).
Advanced online systems exist today that unite many of those resources with additional text-mining and predictive capabilities (e.g. STRING). These are however still insufficient in generating testable hypothesis due to the inherent limitations of web services such as their limited access to local user data limiting potential for high throughput analyses of large sets and failing to provide network analytical tools necessary to fully comprehend them. With data security and confidentiality being a concern in-house and even desktop-based analyses are of advantage.
In order to provide scientists with clear and relatively simple analytics of their data many tools were developed e.g. Cytoscape, CellDesigner, jDesigner, Osprey, Medusa just to name a few, followed by commercial products by Ingenuity, Ariadne/Elsevier, GeneGO. All aim to provide easy and quick integrative capabilities for overviewing complex datasets using graph theoretic approaches. Indeed graph theory, a mathematical concept, has been transplanted and the patient has survived. Biology has, after centuries of denial, turned into a mathematics-rich science with biomedical models as abundant as PCR, fusing together two disciplines most capable of describing life.
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