Monthly Archives: February 2007

Why I think the NCBI Rocks!

A while back I had written about how the NCBI had probably mis-indexed a particular protein domain annotation , because their search algorithm yielded irreproducible and probably erroneous search results for a particular search pattern (see Whassup NCBI) .

Back then I had contacted the NCBI support staff who were extremely helpful and helped me initially troubleshoot the problem to some extent but told me I had to wait for the possible mis-indexing error to get corrected. A few after my initial post I got an email from NCBI support asking me if the problem persisted and whether I had tried repeating the search. I tried repeating the search and the problem had indeed been rectified.

Throughout the whole process I had the good fortune of speaking one on one , with several of the support staff at NCBI who attempted to help me troubleshoot the search pattern. Often these conversations lasted almost 30-40 minutes and contributed immensely to my knowledge of how the NCBI was laid out , the numerous interconnected databases , the precompiled BLAST options , the linkout options and the MyNCBI “personalization” options.

Before this encounter, I did on many an occasion found myself hoping that google would index all the biomedical information out there and make a lot of it available in a “google-ized” format. I am beginning to change my mind on this. Having realized the powerful ways of querying the data at NCBI . I can certainly say that I turn to the NCBI more and more to construct and optimize several queries in the genomic sequence space. The dedication with which the NCBI support staff pursued my problem is something I have only come across on many open-souce forums. In direct contrast a few of my posts to google “support” to get some basic questions on their Google calendar bugs sorted out were largely ignored.

Vertical search is becoming a huge buzzword in this web 2.0 aroused world. Lets face it the NCBI had been our vertical seach platform. Its been around long before the term “search” meant what it is today. It is comprehensive, cross-referenced and annotated to the hilt , has personalization , RSS feeds , email alerts , links to full-text and private libraries all built in for FREE.

In my very humble opinion it has evolved into an extremely powerful and dare I say user-friendly front end to query all biomedical information. If only more of us Omics practitioners take the time to learn its very powerful features.

I for one will definitely try to blog more about its many facets ( along these lines see Search in the Omics age, Compiling search strategies in the biosciences, Screencast 101 ). And I will never wish google waste its time with what the NCBI has already done so well. I only wish the NCBI would popularize its offerings more. I also wish all the bioinformaticians out there would do their part in teaching everyday users the ins and outs of its tools. For now I am glad that we have something a powerful and dedicated as the NCBI.