There have been several major improvements this month in novoseek:

• Select the Publication Type from the Advanced Search panel

Users have been asking for it and it is now available when you are on the Advanced Search panel.


TIP 1: Hold Ctrl (control) to select several Publication Types

TIP 2: Learn more about the different Publication Types and their use when looking for scientific publications.
• Complete authors list for each article

With a view to providing you with more information about the authors of an article, we have updated the meta data of every publication with the complete list of authors.

- In the search results page, you will see the two first authors and the last author of the publication. Check with a search example


TIP: when you are looking for a specific author, this author will appear highlighted within the results and you will see 4 authors in total for every publication (the 3 mentioned previously + the author you are looking for and highlighted within the results) Check with this example for Eley Robert

- In the detail page of an author, all of the authors are now listed. Check authors in a publication detail page


• Disambiguation of authors

A common problem within the scientific literature is the broad range of text formating that has an influence on authors name too. Sometimes an author name is written with Last name, First name or Last name, initial First name, etc. We now index all the known aliases of an author to make searches for an author publication more comprehensive. Check direct example of author disambiguation


• Better navigation from one search results page to another

Users suggested to give a more intuitive navigation menu at the bottom of search results pages to switch from one page to another. This is done!

This is the 3rd and last post of a series of post about the technology behind novoseek. In the first issue we talked about the problem of synonyms, in the second we showed the challenge of dealing with homonyms, in our third issue we would like to share some thoughts behind data organization and its representation which is a common issue to any type of Web application.

I must confess, I am fond of data visualization. I love all those keynotes, or graphics that have great colors, shapes… They catch my attention despite the fact that I might not understand them or that they provide me with irrelevant information. However some of them are really amazing. When I was doing my research on bioinformatics I was desperate looking for ways to represent all the data I had on protein interactions in a way that I could get a big picture at first and then focus on the details. I found a few amazing things at Visual Complexity but not flexible enough. I must confess that I failed in my intention to apply my programming skills to this task.

When I joined Bioalma and I started promoting our first product AKS, I was really excited with one of its main features that represents the relations among concepts based on the co-occurence in the literature. Is a great piece of software that lets you see at-a-glance which concepts are more related and visualize clusters. However, the information behind it was not always understandable.

When we started the novoseek project we decide to embrace the KIS (Keep It Simple) principle. Although we  try to keep up with this philosophy, I must confess that in our meetings the development manager, marketing director and an art director, its hard to say if we are even close to this philosophy.

Regarding the novoseek interface

As you might remember from previous posts, novoseek analyzes all the literature with an algorithm that integrates database information and takes into account the context of terms to annotate them in the literature. So when we started the project and we had all the data from the analysis of all the literature, we asked ourselve “what should we do with it? How could the user take advantage of all this analysis?”. Obviously, putting it in a search engine that is simple, clear and easy to use was our best choice. We needed to start organizing the data and designing a visualization interface to interact with it.

We needed to arrange all that information in a data structure that could give a fast, efficient and scalable service. The scalability issue was a really important concern. We didn’t want to change the data model when the system needed to serve millions of simultaneous petitions.

We also needed to have a picture of what type of information we wanted to display and how the user could interact with it. Based on our experience we knew that we needed to develop something not only simple but also familiar to the end user. We knew that designing an advanced interface with lots of information would be likely to disconcert the users. Our CEO was always telling us “we need to do something that doesn’t need to be explained to use it and understand it”. And so we did.

So the indexing technology and the automatic disambiguation method enabled novoseek to search faster and more efficiently the most relevant documents. We decided to take advantage of that and build what we called Profile. This profile is the result of the analysis that novoseek does taking advantage of the results of our text-mining analysis to build a list of the most relevant concepts to the query. We thought that this list would be really helpful since it gives a quick idea of what are the main themes related to the query. As we thought this list of relevant concepts needed to be interactive, we then added some functionality to it. Whenever you click on one of the terms of the list you get all the documents that take into account the very query term and the clicked concept. You can check examples with our user cases.

After that, we added many other features, some of which are really handy! Others may be a bit more hidden for advanced users that want to make the most out of the system.

However, understanding the users, the way they interact with us, what is useful and what can be removed to keep up with the KIS philosophy is an endless and ongoing process. At Bioalma, we are always studying what would happen if we put this menu here, if we choose this color or if we set up this log-in box there. Indeed, we mix our own craziness with the user suggestions and it is clear that sometimes we come up with a different (or strange) interface. So stay tuned and find out soon the results of our conversation with users and our own schizophrenia.

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)

We are glad to announce the launch of the biomedical gadgets working thanks to the novoseek’s API. The use of the biomedical gadgets is open to everyone and free. You can get your API Key today and start using the gadgets to extract relevant biomedical information from novoseek and to create biomedical gadgets. In order to create biomedical gadgets, you just have to follow a few steps to publish it on your website or blog.

Gadgets will allow you to publish biomedical information where you want. Gadgets can be published on your blog, website…(where scripts are accepted) and will alllow you to easily extract information from the literature according to your query. With the gadgets you will:

• Enrich your content
• Integrate valuable data
• Display more information
• And no need to know about programming.

There are at this time 2 types of gadgets:

• The Key Concept Gadget allowing you to display the information related to any biomedical concept.
• The Document Gadget allowing you to display the most recent documents related to your search.

Through an intuitive interface, you will create handy gadgets in a few seconds and will be able to publish a gadget where you need it and modifying it as many time as you want. You are also able to create multiple different gadgets.

Let’s have a look at the possibilities brought by the gadgets with a few examples:

• Insert a Document gadget on your Diabetes blog sidebar to keep readers updated on the most recent scientific publications.

Example: 10 latest publications for Diabetes.

• Insert a gadget to show the most relevant disease, pharmacological substances, genes & proteins, chemical substances, organisms, organs & body parts, tissues, biological functions, procedures-techniques, journals, authors -a combination of them or all of them- related to your query.

Example: Tissues, Biological functions and Procedures/techniques related to “chronic granulomatous disease”

• Match the gadget design to your blog’s.

The examples shown previously have a style by default but you can easily change the design colors, width and height during the creation of biomedical gadgets.

Last but not least, we recommend you to watch the tutorial video about the gadgets to see how easy it works.

We’d love to hear from you and know how you are using the gadgets, so feel free to contact us or leave a comment below.