Entries from July 2009 ↓

There was much concern some time ago when the swine flu pandemics began to spread from Mexico to the USA and Europe. Then we somehow got overwhelmed by other information such as the Air France flight crash in the Atlantic or Michael Jackson’s death. Now it seems that the swine flu has come back again (or are the medias putting more emphasis on it?) as everyday more people get infected and die. The WHO (World Health Organization) increased the Pandemic level to Phase 6 -equal to widespread human infection- as shown in image below.

At the same time, a strange phenomenon is going on: the swine flu parties. What’s a swine flu party, you’ll ask? It consists of organizing a party where one of the attendee is someone infected with the Swine Flu virus. Therefore it pretends to help healthy people catch the virus and consequently grow immune against it. This very strange and unexpected practice is growing popular among people as we can read on this article on the Independant where this 15 year old girl states that she would “prefer to get it now, rather than next year which is my final GCSE year, and because apparently it’s going to be the winter version of the disease that will be more dangerous“. Reading this I started to look for further information and happened to be very surprised at people starting to organize parties and looking for infected people. A first look at Facebook (a reference when dealing with organizing a party) left me speechless…

Obviously, this practice is growing popular. People argue that they are used to doing the same with Chicken Pox for their children. But are they? Do people really do that?

Let’s get things straight and explain why I think this is an irresponsible behavior. It is understandable that some of the people think it is better to catch it now before it mutates and become stronger. Nevertheless there are way more risks than benefits to this kind of behavior:

• Nobody knows how will the virus act on every single person. We can’t yet plan its consequences and development so it is very risky. As declared Richard Besser (Head of US Centers for Disease Control and Prevention ) “…how an individual person will be impacted by the infection is not something that we know“.
• We shouldn’t forget that once someone is infected, he’s likely to infect more people. Among them, some may be weaker: children, elderly people, pregnant women, with health condisions, etc and be seriously injured by the virus.
• …

For more information on the spread of influenza virus, have a look at this study “Modeling the Worldwide Spread of Pandemic Influenza: Baseline Case and Containment Interventions“.

Now I’m asking you: Would you go to one of them?

If you are used to performing researches with biomedical search engines such as novoseek or Pubmed, you might have noticed that different query terms can lead to the same results among the biomedical literature. Why that? Simply because there are many ways (eg synonyms) to refer to a same biomedical concept (disease, gene, pharmacological susbtance, etc).

The issue with search engines is that almost everyone has its own knowledge and habits when referring to something. Some will give it an explicit name (for instance “breast cancer type I susceptibility protein“), some will give an abbreviation (“BRCA 1“) and others another synonym (“BRCC1“). When it comes to dealing with databases and information extraction, the problem becomes even trickier.

Why is this making the information retrieval more difficult? Because when you are doing a research on biomedical search engine, the system generally retrieves information from one or several databases that compiles thousands of journals. No need to say that each author, each scientist uses its own genes terms accordingly to his field of study and knowledge. As a result, this plurality of terms makes information retrieval difficult as the system is unable to analyze all of them as a whole. Therefore one would read information about “BRCA 1” because the term is mentioned as it comes in the publication but would miss the publications where it is referred as to “Breast Cancer Type I susceptibility” -which is the same!

In order to cope with this problem, what has been done at novoseek is develop a unique information extraction system that based on dictionaries  is able to return the publications no matter the synonym used.

Did you know that, on average, there are 7 synonyms for a single human gene? Interestingly enough to be mentioned, the one which most has reach 164 terms. How do we know that exactly? Because in our databases, we fill in the IDF (for Identifier), FA (for Functional Annotation) and SYN (for Synonyms) for each gene. Based on that, we are able to computate information about each of them.

Let’s see with a search example in both pubmed and novoseek. We are going to try with GLO1 (a glutathione-binding protein involved in the detoxification of methylglyoxal, a side-product of glycosis). This search in novoseek gives 739 results and the search is mapped as GLO1. When clicking on the Gene, a window pops up and shows the synonyms for this term, as shown in the image below.

Performing this search in pubmed returns 204 results and a search for one of its synonyms (Lactoylglutathione lyase) returns more than 700 results.

Now have a look at this very search in novoseek and see how the search has been interpreted.

Interesting isn’t it?

What’s doing novoseek is perform a concept search and analyze all the synonyms (alternative names) to the current search term in order to return all the corresponding results. Obviously, this is making searches easier and more comprehensive as you do not have to look any further. The information extraction process is illustrated below.

You can now understand what is the benefit of this technology of analysis in order to return all the publications no matter the synonym used.

I could tell you now about the importance of context to disambiguate the results and return the publications that you need to read…We will do that in another post!

In ‘There’s Something About Mary‘ (1998), high school senior Ted Stroehmann (Ben Stiller) suffers a tremendous accident triggered by an awkward situation that take place while he is in the bathroom.

This scene came to my head the moment Christian, inspired on a discussion over a post on the conversation on NCBI ROFL blog, sent me a search result in novoseek for penis zipper. I must confess that I was shocked to see that novoseek found 16 Medline articles on the subject and  that the first document goes all the way to the 70s. I guess that what it really surprised me is that in the year 2006 it still seems to be an unsolved problem.

One of my favorite study among the results  was the one from the journal The American journal of emergency medicine comparing 2 different methods of emergent zipper release. In this one, they study an alternate method of zipper release that is up to 65,3 second faster then the standard procedure that goes for 15 seconds over the minute. It as well concludes that the “optimal procedure is also dependent on the location of the entrapped tissue and the type of zipper”. What is also interesting about this study is that it was made with volunteers.  I can hardly imagine being part of them in this type of studies. And on top of that, testing in different types of tissues? wow!!

Anyway, another interesting result is that novoseek didn’t find any awarded grant for this kind of research. Does that mean that it is not and interesting research issue anymore? Has it been solved yet?

I guess that if Ted Stroehmann would have only known a way to get out of his situation in 10,8 seconds it wouldn’t have been such an embarrassment, and the movie wouldn’t have been as funny.