A blog about information technologies in the biomedical sector

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.

1. A search for Addison’s disease via the Advanced Search panel returns 2,563 results in Medline.
2. 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%).

3. Also, the most relevant related Signs and Symptoms indicate: alopecia, fatigue, malaise, cryoglobulinemic purpura, scalp pruritus…
4. We click the “hyperpigmentation” disease and it is added to the current search: there are now 66 results in Medline
5. 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..
6. 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:

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Some time ago, we explained to you how novoseek interprets a query and is able to return relevant publications, no matter the synonym used in the article and in the query. Indeed, the use of synonyms to extend a search makes one of the user’s main goals-and matter-of-factly ours- possible: find the best and most comprehensive information regarding a research area. This appeared all the more important as Techcrunch was pointing out recently that Netbase was giving not relevant – when not really inconvenient – results due to severe problems in their text-mining techniques and semantic knowledge.

However, the path to returning accurate and comprehensive information to the final user is a tricky one. Once the synonyms to a query word have been analyzed, it comes a second challenging  problem: disambiguate homonyms.

Homonyms are terms with the same spelling but with different meanings. When a search is performed, many of the potential results can deal with a totally different area of interest. This forces the user to try with new queries and to make sure that the system is understanding the query correctly; which will avoid further searches.

Obviously, this takes a long time to achieve and it could be summed up in a sentence: “If the search engine would only know the meaning of the search term this process could be reduced to minutes“.

How is the homonyms disambiguation process performed?
Novoseek looks for the word in the literature and based on the semantic role of the word in the sentence and the analysis of the context is able to assign it to an entry in our build-in biomedical dictionary. Below is a sample image of what the context of the spot is with an extract of an article found for BRCA1.

As a result of the analysis, we are able to determine if a document is on-topic or off-topic. For example, CAT is a gene symbol of the human gene catalase, but it is also an homonym for cat the animal or for Carnitine acetyltransferase. This means that if “CAT” appears in a document, a text mining-based system will have to decide to which concept it actually refers and disambiguate the symbol before proceeding to any higher level analysis steps.

Furthermore, there can be an ambiguity as the same gene entity can have the same name in different organisms. As a result the analysis of context information must be able to tell to which organism it is referenced. At this level, it is crucial for a text mining system to get the analyses correct and only associate those documents to a certain biological entity that actually mentions that entity. Errors at this level would populate throughout the system and the end result presented to the user would be wrong.

In regular search engines you will get all documents for a query term no matter its meaning. With novoseek you can focus on the meaning you want for your term to retrieve just the documents you are looking for.

The text analysis is just one of the first steps in nooseek’s text mining technology. The results of these analyses has to be structured and delivered to the user in a fast and easy way.  But we’ll talk about this in another post.

There has been quite a surprise yesterday on the world wide web as the redesigned version of Pubmed was released once and for all all of a sudden, like said Stephanie Fulton on twitter. However this was almost a non-surprise as it was taken off almost right away and made Librarian EagleDawg write about it. In fact, it looks like Pubmed expected technical difficulties releasing the redesigned version of its search engine.

Guys,  we would like all of the Pubmed users to know that we -novoseek- are not responsible at all for this and that we did not touch or unplug Pubmed at any moment .

You can click the image to view it in 1280 x 800 pixels and save it to your computer.

Take the novoseek survey and winAmazon gift cards!

We would like to remind you that the novoseek survey will close in a few days so hurry up to take it and enter the drawING to win one of the 10 Amazon gift cards worth $25 each.

We guarantee you that it takes less than 10 minutes

Thanks in advance to you all for your help… Good luck!

I could have told you about the BioTechnica in Hannover last week in a traditional blogpost (which indeed I did as you can see below), but I prefer to sum it up in 10 words:

1. Huge

The show area is composed of 26 different halls. Hopefully the Biotechnica just occupied 2 of them. You’d better follow the signs in order not to get lost.

2. B32

The exact position of our booth, to be remembered in such a huge complex.

3. Green

The booth color, which actually helped make a difference.

4. Skilled

The people that came visit us, they were either professionals or students who are already used to biomedical online search.

5. Motivating

The feedback we received from them and the ideas they could suggest us.

6. Free

The answer we had to give everytime we were asked “How much does novoseek cost? “.

7. 400

The number of promotionnal items we have been giving away to visitors.

8. 5 hours

The maximum time one can stand without sitting, and it hurts afterward.

9. BioMatters

The name of the company we had next to our booth and we enjoyed speaking with.

10. Seven

The number of beers I managed to drink during those 4 days (”C’mon! I was in Germany“)

If you follow us on twitter or facebook, you may have noticed that we were out at the Biotechnica last week. What’s the Biotechnica? Simply the biggest European show in the field of biotechnologies that takes place yearly in Hannover (Germany).

Obviously, you understand how important it is for us to be there, as we did for major shows in the United States during the year 2009. The importance of the show, the people and companies attending it, its growing influence have made that Bioalma,Spanish -and therefore European- company took the opportunity to go meet professionals, prospects and users from the old continent.

What have we been doing there? Principally meet people and explain them what is novoseek and explain them why it is a great tool. Obviously, some of them would already know novoseek and ask very specific questions.

Nevertheless, one of the main question we were asked, the detail that triggered people’s curiosity is knowing what has to be paid for in novoseek. The answer left them even more surprised as novoseek is a free biomedical search engine. “Free, you have just said? So how do you guys make money?” Well, we make money out of advertisement displayed here and there across the pages on one hand. And thanks to companies announcing via our media platform.

Naturally, we had some time for dinners & bears to follow up with colleagues, users and providers. Its great to be able from time to time to see the faces of people with whom you exchange e-mails, phone calls, twitts…