Knowledge beyond words » Thoughts

What is your path to successful searches in PubMed?

allende — Fri, 26 Feb 2010 13:54:51 +0000

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:

Direct

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

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

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

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.

Direct, this is my path to successful searches in Pubmed
Ask for help, this is my path to successful searches in Pubmed
Alternatives, this is my path to successful searches in Pubmed
Beer, why not?, this is my path to successful searches in Pubmed

Have a great weekend.

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Thank you.

allende — Thu, 04 Feb 2010 11:56:11 +0000

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

A user case inspired by Flash Forward and a poll

Valentin — Fri, 13 Nov 2009 14:21:35 +0000

Flash Forward is unsurprisingly one of the most exciting TV show of this year. As a result, I’m dying to watch a new episode every week. And when I do, I’m having a great time that leads to great discussions at the office about whether this is about future or not and how it can be modified. Nevertheless, I could notice a few weeks ago the interesting case of Edward Ned (also called Ned Ned) whose flash forward vision finds him in a club and having his skin totally black, whereas he’s white currently. Dr. Olivia Benford chooses to treat him as a regular patient no matter his flash forward but Dr. Bryce Varley -her colleague and now totally changed by his flash forward- has another opinion. Indeed, he thinks that this color change may be due to a disease; and that would explain many things regarding this patient. This is why he decides to refer to an online search engine to look for more information.

In order to know more about this Ned’s health condition, Bryce looks for “Pigment Change” in a symptoms search engine. His search returns 107 results and then helps him explain afetrwards that:

- Ned may have Addison’s disease which would explain why he’s black in the future (as he sees himself in his flashforward)
- The disease forces his body make melanine compounds instead of adrenaline
- Without Adrenaline his body is unable to build proper stress response (which explains he’s being so serene)

Obviously, novoseek has different goals (to the webpage Bryce is using) as it offers to explore the scientific literature. Nevertheless we can search for that disease -Addison’s disease- and observe what are the results like.

A search for Addison’s disease via the Advanced Search panel returns 2,563 results in Medline.
Observing the related concepts sidebar we can see that the most relevant diseases related to Addison’s disease are: Adrenal insufficiencies, primary adrenal insufficiency, autoimmune addisons disease, diabetes and Hyperpigmentation (with a relevance of 41%).

Also, the most relevant related Signs and Symptoms indicate: alopecia, fatigue, malaise, cryoglobulinemic purpura, scalp pruritus…
We click the “hyperpigmentation” disease and it is added to the current search: there are now 66 results in Medline
From there, we can start exploring the literature and read interesting publications such as Adrenal autoantibodies and organ-specific autoimmunity in patients with Addison’s disease, Generalized pigmentation due to Addison disease., Long-lasting subclinical Addison’s disease..
The reading of these is a good starting point to know more about the disease, its origins and possible treatments.

Obviously, this complementary information helps save Ned during surgery and Dr. Olivia Benford now has to admit that Ned’s Flash Forward actually helped save him. Based on that, we see the importance of research to know more about a disease, its symptoms and the existing treatments. Furthermore, a search for Addison’s Disease in US Grants could help know what are the current studies about this disease.

And now, I’m asking you:
Note: There is a poll embedded within this post, please visit the site to participate in this post's poll.

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Back to the Daily Grind

Valentin — Thu, 27 Aug 2009 11:53:42 +0000

Madrid in August bears high temperatures and dry air, so citizens of the city scatter to cooler climates such as southern or northern Spain leaving Madrid high and dry (literally). As August comes to a close employees here at novoseek are trickeling in from vacations showing off their tans and telling stories of their time off.

As everyone gets settled back into work they find the innevitably FULL INBOX and VOICEMAIL but eventually you get back in the swing of things and find your “work groove.” So for everyone struggling to get back into their own “work groove” after a pleasant summer vacation, we know how you feel!

Where did you go this summer on vacation? Please, leave a comment giving us ideas where we should go (or not go) on our next vacation!

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Scientific literature helps to avoid tricky situations

allende — Thu, 02 Jul 2009 07:50:40 +0000

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.

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Wolfram Alpha: 5 cons and 5 pros

Valentin — Mon, 01 Jun 2009 11:48:00 +0000

Is it necessary to present Wolfram Alpha, the new online research tool everybody is talking about those days? Obviously not! This is why we prefer to express our thoughts on it in 5 cons and 5 pros about Wolfram Alpha

5 cons on Wolfram Alpha

Wolfram Alpha is not a search engine but a Computational Knowledge engine. What in earth does this stand for?

Easy: Wolfram Alpha is not able to perform searches in an easy way. You have to put search terms with the right and correct words!

What kind of information is available in Wolfram Alpha?

Not a lot. Alpha is very specific. The best you can look for is mathematics, chemical compounds, dates, units or even the temperature in Madrid…Don’t get disappointed, we’ve warned you.

Wolfram Alpha is not clever on the contrary to what it claims to be

Information retrieval is based on a semantics and words tagging. With Alpha, if a word has not yet been tagged for one of its meanings in a context, you won’t get anything of it. What a pity! For example, try to ask it “Who discovered polonium?. It is not able to answer, while in google the same question is easily answered.

Wolfram Alpha is for hype people!

I mean, who is going to ask “How many roads must a man walk down before you can call him a man?” in order to have this result mentioning Bob Dylan. What if we ask “Who is Luke’s father?“, well, here goes the answer namely not much.

Wolfram Alpha is not a resource for biomedical information.

Despite what you’ve heard about it, Alpha doesn’t provide life science publications as novoseek does.

5 Pros on Wolfram Alpha

Wolfram Alpha, this is not a search engine! It’s better.

The way information is treated and presented is far from what you’ve seen and experienced until now. It is not Google nor Wikipedia. It is able to “computate” almost anything you ask it. Try solve a x^2 + b x + c = 0 for x

Wolfram Alpha could revolutionize learning and searching on the internet

Although it takes much to learn how to use it and obtain effective results, it could be an interesting tool for pupils, students and professors.

Wolfram Alpha has some surprises and easter eggs for you to discover.

Here goes the top 10 easter eggs in wolfram alpha. There may be more, it’s up to you to look for them.

The Wolfram Alpha team is working hard to keep it updated.

If there are some failures, be patient and for sure they’ll be fixed soon. The “Give us your feedback” box at the bottom of pages is there for you to point out these.

They are working on making Wolfram Alpha more user friendly

According to statements, they will release an API and more detailed search boxes in order to make searches easier.

Obviously, search engines on the internet are bringing changes and new ways of accessing information. Is this another step towards web 3.0 ?

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Companies & social medias: How far do you listen to your customers?

Valentin — Mon, 25 May 2009 09:52:29 +0000

« How far do you listen to your customers? How are companies getting into social medias?” I have been thinking about asking you for a while now. In your company, do you have set up a platform (a blog, a twitter, a Facebook group, a getsatisfaction account, all of them at once) where they can talk with you? or where you could interact with them? If so, how far will you take into consideration what they say ?

You may be aware of how important are social medias today. You may also acknowledge the importance companies are granting them. Firms that have long been a one way inventing, developing and selling their products are now hiring costly consultants to get into “it“. Of course, “it” refers to social medias, users voice and to a -most of the time- unknown component of management. If they are not doing so, they still can hire a « community manager » or a « twitter manager » in a rush. I am not kidding, this job offer does exist as a twitter internship at Pizza Hut.

Undoubtedly, these jobs openings, this concern to get into social medias seem to be a consequence of several factors somehow connected.

People now have means to speak about a product thanks to the several existing platforms
Gathered in a community or through a communication channel, they have a voice and impact
Firms have discovered (or at least considered) that some people say things about them
And these things they say could either help them think and develop, benefit or do them harm

There comes the interesting part in terms of behavior and consideration towards customers. In your firm, have you developed something anticipating your users’ expectations or just responding to your boss and shareholders’ orders ? Depending on the answer, you are likely to succeed or fail.

In order to listen to your customers and get involved in discussions, there are already some good readings on the subject. I was surprised that when I asked « How far do you listen to your customer » on a our professional Linkedin Group, people would be likely to share their point of views and links. So there are few of them you may want to read :

I agree with statements expressed. Companies should listen to their customers. How far ? I don’t know yet. What is sure is that there must be a good balance between what you want to produce and what our customers’ expectations are. Listen too much to them and you will have the typical “design by committee horse“.

In the field of biotechnologies applied to the internet, listening is something rather new. At novoseek, this is something we put much emphasis on. We have several communications channels open and we try to answer every question that is asked to us. As to development’s needs, we take good care to explain why some of the suggestions are possible while others not. In any case, our Uservoice dedicated platform is the best place to suggest or ask us explanations.

Making long stories short, if you are a service or product’s user, how far do you think they are listening to you? And as a company employee, how far are you listening to them?

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Is the Swine Flu infecting social medias?

Valentin — Thu, 07 May 2009 17:13:41 +0000

Swine Flu epidemics started a couple of weeks ago now and it has been largely covered in social medias. By social medias, I mean all those platforms where one is able to speak and share real-time information about swine flu. Like for other recent and outbreaking news, real-time information has shown its great and useful possibilities. In fact, recently they have been consulted and used to be broadcasted on mainstream channels such as television. I will insist on the “Twitter thing“, but not only and this is why we can talk of social medias.

The importance of Twitter has been largely acknowledged these past months. For example, this man twitting directly about the plane landing in the Hudson river or the Mumbay attacks. These are examples who have settled a new order in information releases. On one because people like you and me would be likely to become reporters -would they want it or not- able to release information and pictures. On the other hand because it would get people involved and react to attacks, threats or needs faster, as it was done for this hospital in Mumbai.

However, Swine Flu is pretty different: the epidemics is best managed by the WHO organization and there is few people like you and me could do besides informing about what is this disease about (H1N1, Influenza, etc). Are social medias information relevant for Swine Flu ? Is everyone entitled to speak about the Swine Flu on real time information platforms and social medias? Are there limits to one’s use of twitter? And, most importantly, are social medias infected with Swine Flu?

I was stuck by the amount of information people have been releasing on Swine Flu, regardless their specialty or their areas of interest. It just seems everybody had something to say and something to share on that matter. I admit that I (as part of the marketing team) decided too to enjoy this phenomenon to put a search example on H1N1 and swine flu in novoseek. But hey, we’re not the black sheep, other search engines did so, I’ll let you guess which ones.

To give you an idea of the phenomenon, let’s check on trends for swine flu in twitter. Obviously it’s been a hot potato on twitter. But not only. And interestingly, searches for this term experimented a great increase…that quickly dropped.

I understand this is something legitimate –getting worried and twitting about it. However not all of the twitts seem to be justified nor important. Indeed, people started joking about it or -even worse- spreading false information. And I sense that the “you can get swine flu by eating pork” comment is about to become a famous example. Trustworthy people have already been writing about it.

Don’t get me wrong, the problem is not in people joking about swine flu but in the information reliability. Since everyone can follow the hot news using the # hashtags in Twitter Search, it triggers a debate. How to find reliable information among users? Who can be trusted? Who should be avoided ? These are questions that matter-of-factly appear to me and should raise your conscience too.

According to the following statistics for Swine Flu in Google Trends we notice that the drop of interest is almost as fast as its rise. Are we dealing with a serious pandemics here, or just some buzz effect? I am wondering…

The fact is swine flu has had its days and information –good or bad- has spread like fire over social medias. People would speak about it on Facebook too. This map shows how people have been updating their status mentioning “swine flu” in it. It has gone west to east.

This is a good illustration of how people started mentioning swine flu in social medias regardless the reliability or truth of information they would state. One more example, people would start making business over it and enjoying the phenomenon, worries or hysteria (no matter how you call it)… It seems like using the Swine Flu keyword was the key to success. You don’t believe me? Have a look at this advertisement in Google when you perform a search for “prevent swine flu“.

You’ll tell me that it’s always been this way, people would tend to enjoy people’s worries and buzz events. But I fear that Swine Flu has reached a new step.

Where are we going with social medias? Is the epidemics matter enough for people to be entitled to tell all sort of things over the internet? Do we have to find a way to select and filter our contacts ? Should we move to other (new?) platforms? There are questions I don’t know how to answer but I’d sure like to have your opinion about.

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How difficult is it to change?

allende — Mon, 20 Apr 2009 15:55:00 +0000

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?

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Free access to biomedical knowledge

allende — Fri, 20 Feb 2009 09:15:10 +0000

Dodo bird

The NIH’s recent measure responds to a paradox in the field of scientific publications. It is the classic “chicken or egg” scenario.

First, much of the content generation is done so at no cost to the “publishing house”. Researchers, sponsored mainly by public institutions – and driven by their own interests and search for knowledge – create new research. The new content creation is usually based on “free” generation, collaboration and assessment of content.

Second, the publishing companies then add value by managing, editing and distributing that content. In this process, “end-user” scientists have willingly paid publishers for the ability to access this “approved” content.

So the paradox before us is…if the free content is based upon paid content (made available through publishing houses), should the new content be made available for free or follow the publishing payment model?

In fact, there is no black and white answer – but new technologies are creating an even more heated debate.

New technologies and the Internet have simplified the editing and distribution processes, opening new possibilities for additional formats and business models, such as open access publications, in which access to contents is free and redistribution is at your fingertips. Will the new technologies be able to handle the role that traditional publishers have successfully handled for nearly 100 years in the areas of managing, editing and distributing that content?

In the new model – what becomes of peer review? In the traditional method, public institutions fund the management and the peer-review editing process, since these publications charge researchers for the distribution and circulation of their work once it is considered scientifically relevant.

Through PubMed Central, the NIH has generated a centralized system aimed to distribute scientific works which have already undergone a peer-review process, and have made scientists sponsored by the NIH add a clause regarding the copyright’s release to publishing companies, before the last version of their work can be placed in this repository 12 months before the publication. Congress’s proposal wishes to avoid this kind of measure.

We must take into account that the research process is strongly supported in the maintained publication of new results, which daily becomes the base for additional discoveries by scientists. Better access to information and the implementation of easier conversations, such as access offered by the Internet would accelerate research, as mentioned by Mr. Akst in The WSJ: “knowledge dissemination is crucial for the creation of wealth and can’t reproduce in isolation.”

It is true that the management of any peer-review process is necessary if willing to maintain the quality and excellence of scientific works, but it is in any case a process in which scientists collaborate voluntarily, a process in which new technologies have enabled a new, easier distribution. And if there is an entity willing to lead the centralization of contents, is it sensible to approve measures not favoring this access to content?

Unfortunately I don’t have an answer. To deny access to valuable medical information, just doesn’t seem right. Neither does denying a commercial business the right to operate when it provides a valuable service.

So – chicken or egg? All I know is this debate is not likely to go the way of the dodo bird anytime soon.

Knowledge beyond words » Thoughts

What is your path to successful searches in PubMed?

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A user case inspired by Flash Forward and a poll

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How difficult is it to change?

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