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 .

This user case is inspired by a search tutorial for Pubmed (see page 61) brought to our knowledge by María, Medical Librarian from Torrevieja Hospital (Spain). We found it interesting to show how novoseek provides results as satisfactory as Pubmed in a simple and quick way.

1. We first search for « tamiflu » in novoseek.There are 840 results in pubmed and 144 in free full text to date.
   
2. Looking in the search details we notice that our search has been mapped to pharmacological substance « tamiflu ».
   Clicking on the the term tamiflu pops up a window with complementary information. This is handy to know the synonyms (alternative names) to Tamiflu : Oseltamivir phosphate , GS 4104 are some of them.

3. We need to look for influenza disease to keep building our search.Obviously, it should appear in the first relevant related concepts to the previous search. Indeed, it is the first related disease to the search Tamiflu. Clicking on it will add it directly to the current search (alternatively you can click on the « i » icon and click on « add filter » as shown on image). The search is now refined and we have gone from 840 results to 639 results in Pubmed.
   
   
   In this case, we are looking for Meta-Analysis publications. In science, “meta-analysis does more than just combine the effect sizes of a set of studies. It can test if the studies’ outcomes show more variation than the variation that is expected because of sampling different research participants” as explained in the Wikipedia. This should help us find publications showing the efficiency of Tamiflu to diminish the percentage of secondary complications.
4. We now need to select the publication type (or type or article).We click on the « bibliographics tab » and where publication type is, we click on the « more » button. Where « Meta Analysis » appears, we click on that term which is directly added to the current search. We now have gone from 639 results to 9 results in Pubmed.
   
   
5. The results are very satisfactory as they contain the same publications as in Pubmed. Should we need to look specifically for publication mentioning children, look for the filter “Homo Sapiens” in the related concepts tab on the left and add it to your search. We now have 5 results in Pubmed.
   • Check more User cases.
   • Check more Tips.


We can compare now these results to Pubmed’s and we notice that we have the 3 publications found in Pubmed in novoseek results. The advantage with novoseek is that we have performed a complex search in a simple way and in no time.

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.

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: