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.

Welcome to the MedLib’s Round 1.9. This month, the MedLib’s Round did not specify a special theme. This may have encouraged medical librarians and you to submit articles as 13 16 people took part in this round. It is always interesting to read medical librarians’ concerns as they are using state-of-the-art tools and techniques to work better and face the new challenges of communication, information retrieval and are always keen on sharing their impression on new services and debates. You will notice that this month, the MedLib’s Round leaves room for discussions on Social Media, web 2.0 services and Tips for health.

Thoughts

• David Eddy Delivers Controversial Reinertsen Lecture About Future of Evidence-based Medicine posted at ICSI Health Care Blog by Kent Bottles, MD.

Dr. David Eddy is a controversial doctor that questions the reliability of evidence-based medicine. He was invited at the Institute for Clinical System Improvements by Kent Bottles, Chief Knowledge Officer at this institute in early november. His conference was remarkable for two reasons. First one is that more than 300 people gathered to attend it. Second is that no one would have guessed Dr. David Eddy would challenge people to think about the future of ICSI and of evidence-based medicine. An extensive post you should read to keep updated on the future of evidence based medicine. (Follow Kent Bottles on twitter)

• Technology & Medicine: new screens on Alisha764’s blog

Alisha Miles shares with us her interest for new technologies and their interest for medicine and health information. In that case, she focuses on the new screens available or on the market or to be released soon and wonders about their possible uses. (Follow Alisha764 on twitter)

Social Media in health

• How Can We Help? Roles for Librarians in Public Health on PH/HA News by Alison Aldrich

Alison exposes her feelings after she attended the American Public Health Association conferences. Her post is a nice sum up of the conference and the people that were there as lecturers. The amount of conferences about social media for health matters lets us guess its importance in discussions. She raises a great question about the importance of advocating open access to public health research too. Indeed, she spent a time in the National Library of Medicine’s booth in the exhibit hall where she could talk about one common question: “how can I get all of your journal articles for free?“.

• What is Google Wave and why should I care? on Krafty Library.

Michelle sums up what is google Wave about and how you can use it. This article will be perfect for you to discover, understand and start using Wave in a proper way. She describes how medecial librarians have already created dedicated waves but still doubts about usefulness of the tool. (Follow her on Krafty)

• Manhunt: Google Wave for Community (Emergency?) Communication posted at Eagle Dawg Blog by Nicole S. Dettmar.

Nicole took part in the google wave about the manhunt in Seattle that happened in early december. She shows how powerful was the very google wave as to information exchange and how users helped enriching previous content. At the same time, she raises the problem of false information in waves (new email tool from google encouraging real time exchange) and spam that may get into these new communication channels. (Follow EagleDawg on twitter)

• FDASM Highlights for UM Stakeholders, pt. 1: Early Presenters as SWOT-Plus posted at Emerging Technologies Librarian by Patricia F Anderson

Patricia wrote a great post (the second) on the highlights of the FDASM. The FDASM is an initiative from the FDA about the use of internet and social media for health related communications for FDA-regulated products. This public hearing held in early november was a beginning to knowing and discovering how to use social media channels to communicate about products. In that field, she recalls how the FDA has already been providing essential resources online. There is more to learn and I encourage you to read it. (Follow Patricia F. Anderson on twitter)

Web 2.0 services for health

• Biomedical search on Biomedsearch by Dr. Shock on Shock M.D.

In this article, we learn with Dr Shock about a new tool that wants to provide free access to documents relating to the biomedical field. He explains the functions of this search engine and wonders about whether it can be an alternative to the redesigned pubmed.

• How to switch from one to the other antidepressant by Dr Shock.

There’s one common problem with antidepressant which is either that the antidepressant does not work or provokes side effects. When that happens, you have to switch from one to another. This can be a tricky task and Dr. Shock presents us some great resources websites to manage it. (Follow Dr. Shock on twitter)

• Medpedia Now Includes News & Analysis, Alerts, Q&A by Walter Jessen on HighlightHealth

Walter Jessen focuses here on new functionalities brought recently to Medpedia and create a richer experience for users. Mepdedia is a medical wiki and has useful functionalities. You will now be able to use in Medpedia the following features: News & Analysis from over 150 professionals, Alerts from real time web platforms and Answers (a kind of medical Yahoo Answers). He then wonders about the possibility for Medpedia to become a medical wikipedia thanks to the amount of reliable information it has. (Follow HighlightHealth on twitter)

Tips

• Adding Methodological Filters to MyNCBI posted at Laika’s MedLibLog by Jacqueline

Jacqueline has created a great tutorial to learn how to add methodological filters to MyNCBI. MyNCBI is one’s account on Pubmed. Obviously, creating filters is a must-use option when you are keen on research and need to automate search processes. In that case, she shows how Pubmed allows to create and run advanced filters to save time. It is always nice to read well detailed techniques that will turn the reader in a better prepared person for searches. Jacqueline writes a lot about Pubmed and she has a great experience with it. Enjoy learning with her. (Follow Laikas on twitter)

• How to follow Twitter users in Google Reader on Clinical Cases and Images Blog by Dr. Ves Dimov.

In this post, Dr. Ves Dimov (who has a great blog in medicine) makes us discover a way to easily read Twitter updates without even following the people via Google Reader. Dr. Ves Dimov explains how this approach makes it easier for him to manage multiple information streams. Plus, Google Reader is web-based and can be accessed from any devide with an interent connection. (Follow Dr. Ves Dimov on twitter)

• How to make and maintain a Library Twitter account on DigiCMB by Guus Van Den Brekel

Guus shows in this example of a new twitter account how to fine tune parameters to receive all the possible interesting updates and twitts right into your twitter account. This tutorial will definitely take you to the best practices in terms of interconnection and follow up! (Follow DigiCMB on twitter)

• Allergy Notes: If you think blogs don’t matter, think again: this blog is the number one search result for “allergic rhinitis guidelines” on Allergy News Updated Daily Blog Dr. Ves Dimov.

Interesting reflexion by Dr. Ves Dimov on the role of blogs when looking for information online through search engines. From the example “allergic rhinitis guidelines” which is the first result on Google, and a blog post -hence listed before NEJM- he shares with us his vision of the future of search results. Blogs and fresh content can play a significant role but better quality source should always be sought for. (Follow Dr. Ves Dimov on twitter)

• A review of the main reference management softwares on Knowledge beyond words by Valentin.

Through a detailed post, we describe the main citation managers available out there and their particularity. You should consult this article if you are to decide what is the citation managers most adapted to your needs and uses. There is also the results of a poll launched on twitter asking people what is their favorite citation manager. (Follow novoseek on twitter)

Thank you for reading this MedLib’s Round on Knowledge beyond words. We’d like to help spread Jacqueline’s message who is looking for ideas for a logo and a new name for the MedLib’s Round which is according to Berci, one of the important things of a blog carnival. So feel free to submit her your ideas, it will be much appreciated.

Feel free to subscribe to the RSS feed of MedLib’s Round Blog Carnival. Next MedLib’s Round will be published next January 5th on Dr. Shock’s blog and you can already submit your materials via this form.

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.

The idea for this post came to me while I was conversing with a relative. She is a medical resident and informed me that she had to start using Pubmed overnight and happened to find it a bit complicated. Consequently, I could confirm that Pubmed is pretty hard for novices to use and took advantage of the opportunity to pitch novoseek to her. Should I remind you that novoseek is a free, easy and intuitive biomedical search engine? Anyway, this discussion with my relative reminded me that some time ago, I heard (thanks to fellow followers present on the MLA in Hawaï) that Pubmed was about to enhance its interface this summer.

This announcement is actually big news for the life sciences community as Pubmed, the search engine of the National Institute of Health, is one of the most used among the choices offered on the web today. Due to the amount of queries it has every day, improving the user experience was something normal and expected. Alisha Miles (a medical librarian for a non-profit hospital in Georgia) declared: “these all sound like wonderful improvements. Hopefully, we will get to a point where we can provide input to NLM before some changes are rolled out“.

Interestingly, these changes aim to make it “easier to use“, will “simplify the interface” and “refresh the look” and offer “better organized text on screen“. It is interesting that Pubmed is moving towards a simpler user interface, as novoseek has been doing this from the beginning.

If you are not familiar with Pubmed, let’s have a look at the screenshot below in order to realize how the layout organized currently.

We acknowledge that a change -as slight as it can be- was necessary. Indeed, Pubmed is difficult to use. It requires learning, training and improving skill to handle it properly. This is why there are many resources (Check this for instance: 18 ways to improve your pubmed searches) and classes about it. The changes will be the following:

1. The tabs will disappear
2. A narrower top banner
3. Combination of Abstract and Abstract +
4. “+” below each citation
5. “Send to” option a lot more visible
6. The right column will be wider and occupies almost 25% of the screen. It will show: the related articles, “Also try” option and recent activity

If you want to have a sneak preview of what it’ll look like you can check directly on David Gillikin’s presentation, although the images are not optimized for viewing on purpose. To make a long story short: Pubmed is about to go a bit more social and current.

Obviously, I have to compare these changes to novoseek’s features. Pubmed currently has more functions than novoseek. However, novoseek has been developed from the beginning with the goal of making it an easy to use, simple and fast biomedical search engine. Now Pubmed seems to be going that way, too.

In addition, we are adding new functions according to your needs. You can now check your search history, save searches and articles, create alerts and manage labels through my novoseek. These are functions we have developed according to the users’ expectations. Indeed, being close to users through twitter, uservoice make interactions and quick answers to their questions possible. We believe it is one of our strenghts against Pubmed.

Should you need to discover how to use novoseek to the best of its ability, you should have a look at the presentation 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!