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.

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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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.

If you are a fellow reader of the blog, or more simply have come once in a while to read us, you must be aware that we are not used to talking about our product on the blog.
However today we feel entitled to make an announcement about novo|seek. Indeed, we have just released new features to the system and we feel the need to share them with you. This new features release is called my novo|seek.

Why « my » you’ll ask ? Simply because now, novoseek takes into account what you are doing when you are using the search engine, thanks to your personal account on novoseek.

Sign up and enjoy your personal space on my novo|seek. You shall enjoy some of the functionalities we have developed for you. What are these new functionalities? They are features you have been asking for since novoseek has been launched and since you have been involved in the development of your new biomedical search engine.

As soon as you are subscribed, you will discover these features :

• Search history
• Save searches and create alerts
• Manage labels
• Manage your account

Users are really enthusiasts regarding these new options as they allow them to go beyond regular searching and make their daily tasks much nicer. Let’s step into each of them to know more about their functionality and their use.

• Search history : no matter what you look for in novoseek, your searches will be marked there. Should you need to retrieve that search where you read that paper, just look for it in your search history.
• Saved searches & alerts : once you are satisfied with a research, you can chose to save it simply by clicking the « save search & create alert » link. Chose the name for saving this search and you are done. Additionnaly, you can set up an alert for this search. Why is this great ? because the alert will let you know when new articles are released in that field.
• My labels : another great option that will allow you to organize one or several set of documents. Imagine that you are working on that research you must prepare for Dr Bradley. Well, you just have to tick the documents you want and apply them the desired label by clicking on « label » and chose one of create a new one.

These are not the only new functionalities you can now enjoy as now you can export citations in the *.RIS format or select articles by publication type.

Signing up is as simple as these 3 steps:

Now, if you want to discover my novo|seek through a tutorial video, watch below:

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!