The other day Valentin and I were discussing how scientists confront the time-consuming task of looking for information in the scientific literature. From my experience as a scientist and from conversations with friends and colleagues, we found out that many of them end up in a frustrating situation when searching and that their path to successful searches in Pubmed can be summarized in one of the 4 following options:

1. Direct

We manage to find results from PubMed although in some cases we have to face the use of MeSH terms. Hashtag #nsdirect

2. Ask for help

After some time facing Pubmed search engine without any success, we decide to ask for help from a colleague or a librarian. Some of our friends told us that they don’t they take this path without trying to do it themselves. Hashtag #nsafh

3. Alternatives

After performing some searches in PubMed and not succeeding in our commitment we just look for alternative search engines like Google, 3rd party pubmed tools or obviously novoseek (we asked our friends they what do you expect them to use besides PubMed. Hashtag #nsalt

4. Beer. Why not?

I mean, after a hard working day, what is better than a beer and face the challenge some other day. Hashtag #nsbeer

Take a look at the image below, its so funny and so real

Now we need you to act! What is your path? Tweet this post to your followers adding the #hashtag that better describes you.

1. Direct, this is my path to successful searches in Pubmed
2. Ask for help, this is my path to successful searches in Pubmed
3. Alternatives, this is my path to successful searches in Pubmed
4. Beer, why not?, this is my path to successful searches in Pubmed

Have a great weekend.

The second of February of 2009 we did our official announcement of novoseek. Now we are a year older. We have learned a lot along the way from our users, partners and competitors. We have gone through some difficult and some really exciting moments. We continue to develop our system in order to give our users an alternative to PubMed that is easier to use and with which you can get relevant results faster.

New challenges are coming up this year. We are anxious to show the new features  that novoseek is going to offer which most of you will love while others will just think “why didn’t I came up with that idea”

Stay tuned and don’t miss this image that represent a few of the things we have been doing this pass year. We hope you like it.

Thank you.!

novoseek, the first year

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.

We have recently added to novoseek new articles from PubMed Central. This new feature provides the ability to access “full text publications” and we have noticed that there is quite some misunderstanding regarding what has actually been indexed. So let us explain it in detail.

Indeed, we have included the Open Access subset of PubMed Central. What is that? Well, Open Access is the free online access to research papers. Obviously, this definition has driven some confusion and misuse of the term “open” access as it is often considered a synonym to “free” access.

The first definition for open access came up at the Budapest Open Access Initiative which was later revised in Bethesda and Berlin. This led to what Peter Suber calls the BBB open access definition for which most of the Open Access Movement agreed on.
The Open Access definition stands around two ideas:

• Free of charge accessibility
• Tears down permission barriers

Consequently, these ideas make distribution, copying and derivative work production possible to anyone.

Interestingly, we’ve observed that most of the time, open access is used as a synonym to free access. This is not quite correct since open access goes beyond just free access to content. For a better understanding of the differences between them, have a look at the graphic below.

PubMed Central is a free peer reviewed digital archive of biomedical and life sciences literature developed and managed by the NIH. It gives free access to articles among which some are open access. As we have discussed in previous posts, the NIH public access policy has ensured the access to published results of NIH funded research. However it does not say whether it has to be through a free access or an open access policy.

In novoseek, we have analyzed with our text mining algorithms the full text of the open access subset and we have made it public. So now you will find full text articles in which you will be able to highlight all the relevant keywords, and enjoy the great features of our technology.

We hope you like this new data set and we will more than welcome your comments and suggestions.

Recently, Luis (General Manager of Bioalma) sent me the TV ad for the new search engine Searchme.com. For those who don’t know it yet, Searchme is a visual search engine that allows you to see the website that you are about to visit. Obviously, the ad is the perfect illustration of what Searchme is able to do for you and what changes it represents. I think it is really interesting and it brings up an exciting discussion. How difficult is it to change our processes? And how often do we change the way we do things?.

Changing is difficult. Just think of the last time you changed your favorite coffee brand you have every morning. When was that? Or the tools and programs you’re used to use on your computer. When was it? And what about your search engine. When was it? No need to give an answer now, but I guess it was a long time ago. And I can’t blame you for that, people tend to stick to what they are used to because:

• they are familiar with it
• they have it under control
• they have spent a great deal of time learning to use it at its best
• they were told to use it when they didn’t know much about them
• …

Even if we know that there are better solutions for a certain task we -you, I, everyone- don’t change that easily. The feeling of not having under control what we are doing is something not many people look forward to. Let me put it another way: change in habits is something that take time and can’t be afforded by all of us. How frustrating is it to notice that once you’re used to something, the trend’s already changed? Will you be one of the people who enjoy what they know or one of the people who enjoy what’s to be discovered?

Well, it is a tough question. For instance, how many times, when you are away from home and see an international food chain restaurant, you smile and think, finally somewhere where I know what I’m going to get?

Those are questions that have been studied and discussed more than once. Christensen CM and Raynor ME, in their book The Innovator’s Solution: creating and sustaining successful growth talk about how difficult it is for products to be successful if they request from the user to change processes. Seth Godin, in his book Purple Cow, puts emphasis on the early adopters and show how they can help one firm, one product, one idea or service spread on the market or not.

Searchme.com is a new visual search engine for the web. Unlike others, the results consist of a web site’s screenshot presented in the coverflow manner. This is a great innovation in visualization as the screenshot loads fast and allows you to skip from one to another in no time.

Antonio Ortiz, a Spanish technology blogger sustains that one of the ways of competing in the search engine landscape is by differentiation in visualization. However is not the only one.

Like Searchme there are many others search engine competing offering new visualization results. (For more information, you can read this comprehensive article on Visual Search Engines)

In the biomedical sector there are several  alternative search engine out there too. Few are based on technology to compete others in visualization and some they embraced semantic technologies to find more relevant results and make the search research process faster and less painful.

Since changing is difficult, do you think that people would change their favorite biomedical search engine for another? To what extent? And you, what would you do?