I have been having a big push over the last couple of months to consider the needs of biocontextualisation of gene list data within a commercial setting. A bioinformatician is not always capable of making a rational decision based on gene names, and even dedicated biologists are swamped by genes that fall outside of their specialist domains – does a collection of differentially expressed genes relate to something good, to something bad, or to something unexpected?
Martini is a pretty good looking solution that was published in Nucleic Acids Research (NAR 2010, Vol 38, p26-38) by researchers from EMBL in Heidelberg. The solution is based on a somewhat clumsy web interface, but the data behind is based on Medline abstract data and more importantly Medline keywords. Some bioinformatics magic, a little creativity and clearly a lot of hard work are then used to condense a set of differentially expressed genes into something that appears (at least superficially thus far) pretty useful and clearly demonstrates superiority over other solutions that are pretty tightly bound to the Gene Ontology.
What about commercial usage? The authors state pretty clearly that the solution is free-for-all! This comes of course with a caveat; is it really wise to upload proprietary gene list data to an external server? While we wouldn’t lose knowledge on molecular structures, there is certainly a risk element here and I imagine that most commercial bioinformaticians will avoid this tool. I feel that the tool also suffers from the need to work with the somewhat loveless web interface. A cleaner R based API would be lovely – perhaps a task for the weekend?
In conclusion Martini looks very appealing, have a clear reason for existence and is certainly something that I will evaluate. I am already tempted to see how I might use the system within an R integration project – straight to paper reporting is the way to go! Have a look at http://martini.embl.de to see what can be done.
