Searching for relevant scientific articles in known to be a common task (more or less difficult depending on the searching knowledge and the tools used) for life sciences professionals. In fact, there are several web-based services, journals and/or paying (password-restricted) platforms to search from. It is often difficult to know the good search strategy (which platform, what keywords, what filters, etc) in the first place. You may find what you are looking for eventually, but you are desperate to fasten this process and make it easier and less resource-consuming. Even if most of us can ask a librarian (you will find valuable information and resources with these 10+1 medical librarians you should read) or have a Pubmed class, life science professionals need to improve their searches. Improving searches can be done through several ways: reading use cases, tips, using novoseek and, last but not least, knowing what kind of publication type you are looking for. Indeed, filtering a search in Pubmed database by one or several publication types will help you limit a large amount of search results and find what you need to read faster.

This list aims to help the life science professionals determine what the publication types correspond to and what they will allow them to find within the biomedical literature. We will put emphasis on the main and most common publication types you can find while searching for scientific articles in the biomedical literature. Each Publication Type is illustrated with an example on novoseek.

On top of that, we would like to present interesting facts as dealing with huge databases allow us to play around with figures and interpret them. For example, from the nearly 19 million articles available in Medline to date, nearly 97% are categorized as Journal Articles and more than 8% account for english abstracts. However, an article can be categorized in several publication types at the same time. The following image shows how the literature is categorized in publication types.

note:the publication types accounting for less of 2% are not shown in this graph and are gathered in the category “rest of publication types”.

• Clinical Trial


A Clinical Trial is a work that is the report of a pre-planned clinical study of the safety, efficacy, or optimum dosage schedule of one or more diagnostic, therapeutic, or prophylactic drugs, devices, or techniques in humans selected according to predetermined criteria of eligibility and observed for predefined evidence of favorable and unfavorable effects.
Example: BRCA1 – Clinical Trial

• Comparative Study


A comparative study is a study in which a participant is randomly assigned to one of two or more different treatment groups for purposes of comparing the effects of the treatments.
Example: BRCA1 – Comparative Study

• Comment


A Comment is a work consisting of a critical or explanatory note written to discuss, support, or dispute an article or other presentation previously published. It may take the form of an article, letter, editorial, etc. It appears in publications under a variety of names: comment, commentary, editorial comment, viewpoint, etc.
Example: BRCA1 AND BRCA2 mutation – Comment

• Controlled Clinical Trial


A Controlled Clinical Trial is a work consisting of a clinical trial involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or procedures studied for diagnostic, therapeutic, or prophylactic effectiveness.
Example: Sinusitis – Controlled Clinical Trial

• Consensus Development Conference


A Consensus Development Conference is a work that consists of summary statements representing the majority and current agreement of physicians, scientists, and other professionals meeting to reach a consensus on a selected subject.
Example: Asthma – Consensus Development Conference

• English Abstract


An English Abstract refers to publications that have been written in a language different from English and which abstracts and title have been translated to English for indexing reasons in NKM. When browsing results, you can notice the English Abstracts directly thanks to the bracket in the title.
Example: Asthma – English Abstract

• Evaluation Studies


An Evaluation Studies is a work consisting of studies determining the effectiveness or utility of processes, personnel, and equipment.
Example: Asthma – Evaluation Studies

• Guideline


A Guideline is a work consisting of a set of statements, directions, or principles presenting current or future rules or policy. Guidelines may be developed by government agencies at any level, institutions, organizations such as professional societies or governing boards, or by the convening of expert panels.
Example: Asthma – Guideline

• Journal Article


Journal Articles are the predominant publication type for articles and other items indexed for NLM (National Library of Medicine) databases.
Example: BRCA1 – Journal Articles

• Meta-Analysis


Meta-Analysis are works consisting of studies using a quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc. It is often an overview of clinical trials.
Example: Asthma – Meta Analysis

• Multicenter Study


A Multicenter Study is a work consisting of a controlled study executed by several cooperating institutions.
Example: Asthma – Multicenter Study

• Practice Guideline


A Practice Guideline is a work consisting of a set of directions or principles to assist the health care practitioner with patient care decisions about appropriate diagnostic, therapeutic, or other clinical procedures for specific clinical circumstances. Practice guidelines may be developed by government agencies at any level, institutions, organizations such as professional societies or governing boards, or by the convening of expert panels.
Example: Asthma – Practice Guideline

• Randomized Controlled Trial


A Randomized Controlled Trial (RCT) is a work consisting of a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table.
Example: Asthma – Randomized Controlled Trial

For further information and benefits on RCT, I strongly recommend you to read the post “the best study for dummies” by Jacqueline Limpens.

• Research Support, NIH, Extramural


Research Support, NIH, Extramural, refers to publications of research resulting from extramural research funded by the National Institutes of Health.
Example: Asthma – Research Support, N.I.H., Extramural

• Review


A Review is an article or book published after examination of published material on a subject. It may be comprehensive to various degrees and the time range of material scrutinized may be broad or narrow, but the reviews most often desired are reviews of the current literature.
Example: Asthma – Review

• Validation Studies


A Validation Study is a work consisting of research using processes by which the reliability and relevance of a procedure for a specific purpose are established.
Example: Asthma – Validation Studies

Regarding novoseek functionalities, it helps you filter by Publication Type easily as we explain in this TIP blogspot and you can refer to the following images to see where to filter by Publication Type when you are on the results page and where to identify the Publication Type when you are reading a publication on novoseek.

Resources: PubTypes, research, novoseek and insights from José Cristobal Buñuel .

Boolean logic is a system for logical operations, used in many systems. In novoseek, Boolean operators can be used to combine different search terms. Why is this interesting for novoseek users? The use of Boolean operators will help save time and get better results in the first place. There are 3 Boolean logics you can use in novoseek: AND, OR and NOT. Obviously, you can combine one or several of them, as we will show you in the following examples.

• Boolean AND

Boolean AND is used in novoseek to spot publications where both search terms are mentionned.

Cancer: 1,168,270 results
Breast: 259,863 results
Cancer AND Breast: 166,624 results (view online)
• Boolean OR

Boolean OR is used in novoseek to spot publications where at least one of the search term is mentionned.

Cancer: 1,168,270 results
Breast: 259,863 results
Cancer OR Breast: 1,261,509 results (view online)
• Boolean NOT

Boolean NOT is used in novoseek to spot publications where the first search term is mentionned and the one following NOT is excluded.

Cancer: 1,168,270 results
Breast: 259,863 results
Cancer NOT Breast: 1,001,646 results (view online)
• Combination of Boolean operators

The combination of several Boolean operators allows to perform complex searches at once. It is recommended to advanced users willing to save time and read relevant results quickly.

Cancer: 1,168,270 results
Breast: 259,863 results
Trastuzumab: 2,837 results
Cancer AND Breast AND Trastuzumab: 2,184 results (view online)
Cancer AND Breats NOT Trastuzumab: 164,440 results (view online)
Cancer OR breast OR Trastuzumab: 1,261,631 results (view online)
Trastuzumab NOT Cancer NOT Breast: 122 results (view online)

Filter the results of a biomedical search by publication type is something users are really looking forward to finding on novoseek (as this request on uservoice shows, for example).

This inaugural post for tips pretends to help you improve searches in novoseek and especifically describes how to select the publication(s) type(s) you need to read for your search, step by step.

1. Perform a search in novoseek

In this example, we have searched weight loss and we have the following: 72,877 results.


2. Click on the Bibliographics tab at the top of the left sidebar

Clicking on the Bibliographics tab displays the relevant Authors, Journals and Publication Type to your search. Currently, there are 72,877 results for this search.


3. Look for Publication Type at the bottom of list

When you are there, we recommend to click on the more button to display the whole listing of publication types. In that case, we need to read the Review-related articles to weight loss. It’s the 6th concept in the Publication Type’s.


4. Click on the Publication Type you need to read for your search

Clicking on Review will automatically add it to your current search and display results for weight loss in the intended publication type. Here, we went from 72,877 results for weight loss search to 8,217 for weight loss review articles.


5. Modify your search to your needs

You can modify your search quickly and efficiently. If you want to go back to the results for weight loss, just click on remove next to “review”, click on the Bibliographics tab again and select the intended Publication Type.

We are aware that being able to filter by Publication Type is a key feature. We are working on making it easier for you to find it and perform quicker and more efficient searches. We are open to your suggestions in terms of tips needed in order to help you improve your searches so feel free to comment below.

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.

The reference management software -also called citation management software, citation manager or personal bibliographic management software- are programs that allow users –researchers, scholars, authors- to save, work on and use bibliographics citations. The aim of these reference management programs is to save search results and publications with a view to using citations (references) to generate bibliographies. Indeed, publishers or journals often have different citation formats which is time-consuming  activity when writing. These citations management systems help manage bibliographic references and include cited sources easily. In addition, exporting the document to the format needed is also made easier. On top of that, we understand the importance of these software as the scientific literature keeps growing faster.

The picture from PhD Comics should convince you that writing and managing references is one big and hard task!

Why is this kind of systems growing popular and mandatory in the scientist and scholars’ lives today ? There are several reasons to this however two are really important and meet the need to :

• Benefit from effective tools in a world where publications grow rapidly. Indeed, the scientific literature is growing rapidly those last years. For instance, there are 2,000 new publications every day on average.
• Be able to handle all the data attached to a publication : Journal, authors, dates, asbtracts, tags, PMID, etc…

There are already a lot of reference management software available on the market. In fact, there are so many citation managers that one can get lost easily (a look at the comparison of reference management softwares on wikipedia will convince you). Some of them are better known and benefit from good customers’ feedback and reviews. However not all of us know them so we have established this list for you to choose. Interestingly, most of them are free and web-based. Therefore they are accessible from anywhere through private account and remain free.

We will present the main reference management softwares you should know and then show the results of the poll launched on twitter:

• CiteULike
• Connotea
• Endnote / Endnote Web
• Refworks
• Mendeley
• Zotero
• Papers
• [POLL RESULTS] What citation manager do you use?

• CiteULike


Developer: Cite U Like is a free reference management software by Oversity and sponsored by Springer.
Price: Free.
Description: CiteULike is fusion of Web-based social bookmarking services and traditional bibliographic management tools launched in 2004. It is very close to Connotea as you can tag documents too. This way users should try Connotea and CiteULike and decide by themselves. One thing we really like is the possibility to establish priorities for an article you have just bookmarked. (Top Priority ! I really want to read it ! I will read it ! I might read it ! I don’t really want to read it ! I’ve already read it !).
We like: Lately they have come up with a new function that recommends articles to the user based on his preferences and other people’s bookmarks. It’s experiencing a great acceptance among users as they explain on the CiteUlike blog
Twitter: @CiteULike

• Connotea


Developer: Connotea is the free web based service developed by Nature Publishing Group and launched in 2007.
Price: Free.
Description: Connotea works as a combination of both delicious and a reference management system. Registered users are able to tag documents in order to retrieve them later. You can read their blog to keep up to date on their actuality.
We like: Good thing is that you can look for documents tagged by other people as long as their libraries are public which allows you to broaden your searches and knowledge.
Twitter: @Connotea

• EndNote / EndNote Web


Developer: Endnote is a comercial software developed by Thomson Scientific.
Price: It costs approximately $300 for a year’s account.
Description: Endnote is the most known reference management software as it is also a pionneer in its domain since it was first released 20 years ago in 1988. This is the reference management software you would typically find in your university for instance.
We like: With the growing importance of data portability, Endnote released a Web version called Endnote Web. Endnote Web is easier to use and offers slightly less functions than Endnote. For instance you will be able to save up to 10.000 references. Another advantage is that it’s much cheaper. One of the key features of the traditional EndNotes is the possibility to change the reference format in your Word draft, to adjust it to the  journal reference format of the journal.
Twitter: @EndNoteNews

• RefWorks


Developer: Refworks is a commercial web-based service launched in 2001 by Proquest.
Price: You can try it for free for 30 days and then pay approximately $100 a year for one user (sort of expensive).
Description: It is a « an online research management, writing and collaboration tool — designed to help researchers easily gather, manage, store and share all types of information, as well as generate citations and bibliographies » This web based service allows to share references and bibliographies via Refshare (link) . It also support a lot of formats for importing and exporting.
We like: The RefWorks online store where you will find all the items to show your support.
Twitter: @Refworks

• Mendeley


Developer: Mendeley is a research management tool for desktop & web.
Price: Free.
Description: Launched in 2008 by some of the people who have participated to Skype, LastFM and Warner Music, it is told to be the «Last FM of research ». It is growing very popular and they claim to already have more than 100.000 users, as they explain on TechCrunch.
Mendeley works either from the web platform or through the software program. It is totally free and the main difference to a program like Zotero is that it extract information from PDF. The program is powerful and allows to organize documents in a smart way. You can favorite publications, create collection and share them with your community. They also have developed a plugin for word -as endnote does- to generate bibliographies in a simple way.
We like: the « explore research trends and statistics » allow you to discover and aggregate anonymous statistics and trends. Keep up to date reading their blog
Twitter: @Mendeley_com

• Zotero


Developer: Zotero is a free Open Source reference management software Add on for firefox.
Price: Free.
Description: This one differs totally from the previous citation managers (or reference managers software) as it is a plugin for Firefox that is completely free and open source. Since it is a firefox extension, what you download is in Firefox all the time. This may be a problem when you are using several computers. One great feature (maybe the greatest) is that when you are viewing an article that is available for saving, a tiny icon is shown next to the URL. Clicking on it automatically saves it with all the corresponding fields.
We like: Last but not least, Zotero allows you to save into folders, tag documents, search as you type, import endnote collections and is free. Should you need to know more, consult their blog.
Twitter: @Zotero

• Papers


Developer: Papers is a commercial reference management software (available for Iphone) developed only for Macs.
Price: You can try it for free for 30 days and then buy it for 29€. (7,99€ for the Iphone app)
Description: It was launched in 2007 by Alexander Griekspoor and Tom Groothuis while they were studying at the Netherland Cancer Institute. To make this description simple, it is like endnote but exclusively for Mac OS.
We like: On top of that, they have developed an iPhone app so you can manage your citations directly from your preferred mobile. It will cost you only 7,99€. Feel free to read their actuality.
Twitter: @Mekentosj

At this moment novoseek supports a direct export to two of the main reference platforms: CiteUlike and Connotea. You can try it by yourself from this publication on novoseek.

Last but not least, we asked people on twitter which is their favorite citation managers to use and the results are the following (thank you to the almost 100 tweeps who asnwered):

It seems that Zotero is the leader with Endnote while Mendeley is increasing strongly its market share. Other citation managers were also mentionned: BibTex, Wizfolio, Bookends, Bibdesk, Jabref, Citavi. I would be curious to hear what their developers have to say to make us feel like trying them.

This selection of reference management softwares is personal and we will be happy to consider including more of them in the future updates. Just feel free to leave a comment below.