At novoseek, we are determined to making your daily searches for biomedical literature a better, easier and quickier experience. (and this is why we use to write tips, use cases and improve novoseek)

For that reason, we have created a handy my novoseek guide for the members to enjoy the features of my novoseek at its best. If you haven’t signed up yet for a free account on novoseek, feel free to sign up now.

Feel free to download it and see what it has to offer you.

This is the first version so please tell us what other information you would like to read in it.

We recommend you to read:

• Data organization and interaction
• The importance of context in text disambiguation
• Tip #3 to improve searches in novoseek – use labels to organize your readings
• Why Publication Types matter when looking for relevant scientific literature in Pubmed
• Tip #2 to improve searches in novoseek – use Boolean operators

There is one handy tool in novoseek that helps you create email alerts to keep updated and be notified of new papers in which may appear the query previously entered. Indeed, my novoseek users can easily create email alerts any of the searches they perform on novoseek biomedical search engine. These email alerts can be created after a search has been performed and they can be easily edited from your personal account on novoseek. There are a lot of possible uses: simple search for a biomedical concept (eg: a disease such as “asthma“), complex searches that require the use of filters and may require more time to achieve (eg: “Methacholine & Chronic obstructive pulmonary disease in Clinical Trial articles in Pubmed“), for a journal you are reading regularly (eg: “Journal of the American Geriatrics Society“) or for an author relevant in your field (eg: “Collins, Francis S.“).

1. First, save the search you have performed.

In order to create email alerts, you must first perform a search. When the search results are satisfying and you want to create an email alert accordingly, simply click the “save search and create alerts” button at top of results page. A box pops up and offers you to custom the name for this saved search and to save it.


If you haven’t signed up for a free account on my novoseek or aren’t yet connected, feel free to do so in a few clicks.
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2. After saving the search, novoseek offers you to create an email alert for this very search. Click the “create alert” button.

3. Adjust the sending parameters

You are taken to your personnal account on novoseek in the “alert details” category where you can fine tune the alert details.



The parameters allow you to receive email alerts as follows:

• Once a month, and specify on which day
• Once a week, and specify on which day
• Every Day
• The format: HTML or text
• The report format: Title, Short Fragment Text, Sentences or Abstract, depending on the amount of information you want to read in your inbox
• The number of items you want to read in every email alert
• Specify if you want to receive an email even if there is no new articles for your search query
• The corpus you want the articles to be searched in: Pubmed, Free Full Text or U.S. Grants





4. Create email alerts and managing them allow you to consult your existing alerts anytime and adjust their parameters from your personal account on novoseek.

Simply go to the My saved search and alerts panel on your account. From there, you can modify the names of your saved searches as well as adjusting parameters by clicking on the clock image .

Want more Tips to improve your searches in novoseek? Need more help? Just feel free to leave a comment below!

We recommend you to read:

• Why Publication Types matter when looking for relevant scientific literature in Pubmed
• How to create biomedical gadgets in a few steps
• Use case: Is Low Vitamin D Levels Associated With Greater Risk of Relapse in Childhood Multiple Sclerosis?
• Your handy my novoseek guide v1.0
• A surprise for our fans on Facebook

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.

We recommend you to read:

• The importance of context in text disambiguation
• Your handy my novoseek guide v1.0
• Why Publication Types matter when looking for relevant scientific literature in Pubmed
• Tip #3 to improve searches in novoseek – use labels to organize your readings
• Tip #2 to improve searches in novoseek – use Boolean operators

As we know, Bioinformatics is the application of information technology and computer science to the field of molecular biology. Its main purpose is to increase our understanding of biological processes, which is why bioinformatics is constantly evolving and reinventing itself through new discoveries and technology. Some of the major research topics in the field of bioinformatics are sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies and the modeling of evolution. Continuing our efforts to provide our readers with information that might be of much interest in the simplest possible way, as we have previously done with blogposts such as 10 Science PhD Related Blogs or 10+1 Medical Librarian Blogs.

via fujito

We thought it would be helpful to share some interesting bioinformatics blogs that can keep you up to date with all kinds of advancements that are being developed in this area and can also help you find information on new software and data mining systems. These are our picks for the Top 15 Bioinformatics Blogs in 2010:

Fisheye Perspective: A Blog about Systems Biology, Bioinformatics, Chemoinformatics, Science and Life in general- by Abhishek Tiwari.



About the author: Abishek Tiwari shares his opinion on issues dealing with bioinformatics. He is a passionate follower of this subject as part of his research interests, studied B.Tech in Bioinformatics in India and is currently getting his PhD in New Zealand.

Description: This blog includes interesting information on other topics such as: chemoinformatics, visual analytics, systems biology, and science as a whole. One of his latest posts, Availability decay of Bioinformatics web resources: Yes widgets can change it, talks about the inaccessibility of bioinformatics software and web resources and how the use of widgets can improve this situation.


Website: http://www.abhishek-tiwari.com


Twitter: @abhishektiwari

What You´re Doing is Rather Desperate: Notes from the life of a bioinformatics researcher



About the Author: Currently located in Australia, Neil Saunders finds a profound joy in science, which he shares through his blog and other publications. The story behind this blog’s name is pretty funny… after Neil gave a speech at work, “come question time, a member of the audience raised her hand and said: It strikes me that what you’re doing is rather desperate. Wouldn’t you be better off doing some experiments?”


Description: We find this blog to be very helpful since Neil spreads his knowledge, research, and new findings to all of his followers. You can find useful information on database-related issues when visiting this blog, where you can also ask questions on topics he is currently or has previously been researching such as biotechnology and biomolecular sciences.


Website: http://nsaunders.wordpress.com/


Twitter: @neilfws

Blind Scientist

About the Author: In Paulo Nuin´s website, www.genedrift.org, you can find information on this bioinformatician´s work, research, sample software tools, and more! Paulo Nuin, Brazilian born bioinformatician finds himself in Canada getting his post-doc.


Description: In this blog, Paulo shares his insight on creating simple Python scripts. He is very well-recognized in the bioinformatics field and Python programming and was asked recently to review a Python Beginner guide from Packt Publishing. If you want to read more about it, take a look at Preview of Python Testing’s beginner Guide.

Website: http://blindscientist.genedrift.org/category/bioinformatics-opinion/


Twitter: @nuin

Yokofakun: A blog about bioinformatics, semantic web, comics and social networks



About the Author: A blog mainly about bioinformatics and the semantic web. Pierre Lindenbaum is a brilliant bioinformatician from France who is very active in social networks. He also includes comics in his blog, which he has constantly been working on since 2005.


Description: Yokofakun is highly recognized throughout the bioinformatics community through social networking tools. You can find a lot of information about software and databases, as well as overviews and tips on their use. A perfect example of his work is found in The Path from EgonWillinghagen to Neo4j, a graph API fro java: my notebook. We encourage you to follow this bioinformatics blog where you can find many interesting codes.


Website: http://plindenbaum.blogspot.com/

Twitter: @yokofakun

DigitalBio: discovering biology in a digital world

About the Author: Dr. Sandra Porter, a bioinformatics teacher in Seattle and President of Digital World Biology, writes about things she is learning and discovering about in this field of study, and gives her opinion on current events that are relevant to the subject matter.


Description: In her article, A ScienceOnline 2010 session mash-up review: Fact checking and trust, she analyzes whether Google sites contain misleading information while searching for biomedical terms. We encourage you to visit her site and share your personal opinion with her community.


Website: http://scienceblogs.com/digitalbio/


Twitter: @digitalbio

Your bones got a little machine (Pansapiens): Ideas are cheap, implementation is expensive; act accordingly.

About the Author: Andrew Perry is an Australian structural biologist and bioinformatician, and this blog´s author.


Description: Mainly dealing with structural bioinformatics and biology, the content found in his blog provides interesting information of current events taking place in these fields. If you are also interested in video games, Andrew writes web applications and games mostly through Python programming. During 2009, his activity took place mainly in Friendfeed and not in the blog itself. Here are the 2009 posts that never made it where you can find information on database services, API´s and much more!


Website: http://blog.pansapiens.com/


Twitter: @pansapiens

Saaen Tist: On bioinformatics and personal productivity



About the Author: A blog on bioinformatics and personal productivity by Flemish bioinformatician, Jan Aerts, who describes himself as “a genetics/genomics researcher who accidentally tumbled down the slope of programming and bioinformatics“.


Description: Focuses on relevant database and software technologies, sharing his experience and opinion after using them. In one of his latest posts you can find information on the 1000 genome project, the kind of input data it includes, and how it would look in a database.


Website: http://saaientist.blogspot.com

Twitter: @jandot

Byte Size Biology: The musings and ravings of a computational biologist about science, computers, music and, you know, stuff

About the Author: With about 5 posts per week, Professor Iddo Friedberg from the Miami University in Ohio, keeps us aware of all kinds of facts dealing with the scientific world using a humoristic approach.


Description: Apart from science, this computational biologist also shares his thoughts on computers, music, and other topics. Iddo also recommends his favorite bioinformatics blogs. One of the blogposts we have enjoyed the most is A Sh*tload of Data , where he talks about understanding the role microbiomes play.


Website: http://bytesizebio.net/

Twitter: @iddux

It´s Not Easy being Genes

About the Author: For all of you Python lovers! Chris Lasher provides information related to genetics, bioinformatics, and computational biology, which are all subjects he studies as a graduate student in Virginia Tech.


Description: Check his blog out for tips on the latest technology in Python.


Website: http://igotgenes.blogspot.com/


Twitter: @gotgenes

Manuel Corpas´Blog: Genomes, Internet, Bioethics and More…



About the Author: Manuel Corpas is a Spanish computational biologist who shares his knowledge through his personal blog where you can find information on many related subjects of interest such as biology, biotechnology, computational bioethics, synthetic biology and more, where we find he is “a lead developer of the DECIPHER database, a “DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources”. We are delighted to see one of our fellow countrymen so active in the bioinformatics landscape!

Description: You can find posts such as 10 Sarcastic Rules on how to be a Bioinformatician, which not only brings humor to what you are reading but gives you useful tips on how to be at your best. It’s a very reliable source of what goes on in this scientific world.


Website: http://manuelcorpas.com

Twitter: @manuelcorpas

Mailund on the Internet: Computer science, bioinformatics, genetics, and everything in between

About the Author: Thomas Mailund, a research associate professor at the Bioinformatics Research Center in Denmark, is very involved in the bioinformatics world and shares his experiences in conferences and workshops, which he attends, as well as other relevant information on hot topics in this field.


Description: This blog can keep you up to date with information that is emerging in these sessions Mailund participates in. One of his latest posts, which we found to be quite interesting, deals with the evolution of health and medicine .


Website: http://www.mailund.dk/ You can also visit his official work homepage for more information.

Blue Collar Bioinformatics

About the Author: Brad Chapman, biologist and programmer, works in the biology department at Massachusetts General Hospital in Boston. His blog offers support to researchers by answering interesting biological questions, using his personal criteria.

Description: In this site you can find blog posts where he shares information about database systems, genes, and other topics that can be helpful for biologists in their daily functions.


Website:http://bcbio.wordpress.com

Friendfeed: http://friendfeed.com/chapmanb

Mass Genomics: Medical genomics in the post-genome era



About the Author: Dan Koboldt is a highly qualified biologist who works in a Genome Sequencing Center in Washington University in St Louis, and keeps us up to date with this subject through his blog, also sharing his many publications on this interesting topic.


Description: This blog focuses on everything dealing with genomics, just like its name suggests Cancer genomics is one of the subjects he focuses on. In one of his most recent posts, Koboldt points out many concepts and issues that were addressed at sessions in Washington University, such as next generation sequencing and molecular techniques.


Website: http://www.massgenomics.org/

Omics! Omics!:A computational biologist’s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery

About the Author: Computational biologist Keith Robinson has worked on genomic and proteomic technologies, currently working in Massachusetts in the cancer drug discovery field.


Description: Through his blog, Robinson shares his findings by using peculiar examples, which will without a doubt leave you yearning for more. Read his latest post on the possibility of sending synchronous messages to actors…quite entertaining!


Website: http://omicsomics.blogspot.com/

Bonus!

Our #15 Top Pick for bioinformatics blogs is Bio Star available at http://biostar.stackexchange.com/ A site for finding information about bioinformatics, computational genomics, and system biology, containing hundreds of questions and answers on these subjects. It’s an extremely helpful tool, which allows you to interact with other individuals that might have your same interests and doubts regarding bioinformatics. We highly recommend it!

After taking a look at this Top 15 Bioinformatics blogs in 2010, we encourage you to try the novoseek’s API, which we think is a great resource to enrich content, integrate data, and display information in your own format. We are eager to see what skilled bioinformaticians will come up with.

We recommend you to read:

• Interview with Christian Blaschke, scientific director of novoseek
• Social media, web services and tips for health in MedLib’s Round 1.9
• Hello world!
• Your handy my novoseek guide v1.0
• Data organization and interaction

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 .

We recommend you to read:

• Data organization and interaction
• The importance of context in text disambiguation
• Use case: Is Low Vitamin D Levels Associated With Greater Risk of Relapse in Childhood Multiple Sclerosis?
• Your handy my novoseek guide v1.0
• Tip #4 to improve searches in novoseek: Create email alerts

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.

We recommend you to read:

• Your handy my novoseek guide v1.0
• Tip #3 to improve searches in novoseek – use labels to organize your readings
• Data organization and interaction
• Why Publication Types matter when looking for relevant scientific literature in Pubmed
• Tip #2 to improve searches in novoseek – use Boolean operators

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.

We recommend you to read:

• Social media, web services and tips for health in MedLib’s Round 1.9
• Your handy my novoseek guide v1.0
• Interview with Christian Blaschke, scientific director of novoseek
• Tip #3 to improve searches in novoseek – use labels to organize your readings
• Data organization and interaction

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.

We recommend you to read:

• Data organization and interaction
• Your handy my novoseek guide v1.0
• Why Publication Types matter when looking for relevant scientific literature in Pubmed
• Tip #3 to improve searches in novoseek – use labels to organize your readings
• Tip #2 to improve searches in novoseek – use Boolean operators

Research -medical, biomedical, scientific- is one tricky task medical librarians are here to help you with. It requires training, a strong medical knowledge and advanced computer skills. This is why university, hospitals, private and public companies have libraries with qualified medical librarians who help make one’s daily work easier. Indeed, a medical librarian is trained and keep updated continuously on state of the art research. With the internet, the Medical Librarians have understood how web2.0 technologies would help search, organize and work more efficiently. This is one of the reasons why they are online and are used to posting on their blogs. In fact, medical librarians often have a blog and post about the news and share information about new or existing tools.

This is why we have decided to list 10 top medical librarians blogs you should read to get started.

1. A medical librarians exploration of the web 2.0 world and beyond



Who?
Jacqueline is a married librarian with 2 daughters. She studied Medical Biology and worked as a scientist after graduating a PhD back in 1990. She studied a post-doc course documentary information science (1994-1995) and worked as an information specialist in a pharmaceutical company. She now has been a medical information specialist at the Academical Medical Center (AMC) in Amsterdam for 3 years. Also, she enjoys riding her bike everyday.

What?
She is a clinical librarian so she is involved in developing courses, teaching & searching. She first started the blog as a way to publish the class exercises. However she quickly moved to broader interests and caught the “blogging” virus. According to her About page, she tries to blog about medical librarianship, medical information, EBM and Cochrane Collaboration (where she works as a Trial Search Coordinator).
Jaqueline blogs about her feelings about the web2.0 tools, its evolution and gives well-detailed opinions. Reading a blog post takes some time as they are most of the time quite long but they are worth it. They are well structured and often come with web links that help understand better why she came to that conclusion.

We like:
The Blog Carnival that she helped populate and which is held every other month. The principle is that a medical blogger hosts a round and writes a blogpost based on the posts that were submitted before. We invite you to read the latest round now and see what it is like.

Resources: http://laikaspoetnik.wordpress.com/

Twitter: @laikas

2. Emerging Technologies Librarian



Who?
Patricia F. Anderson is a librarian from the University of Michigan Health Sciences Libraries. She used to work as a Head Librarian for the UM Dentistry Lab which helped her enter the wonderful world of social media tools. She is a mother and has a fulfilling life as her Flickr Gallery lets us guess.

What?
Patricia writes pretty much about everything around social media activities, services and stories. Her latest post when writing this review was about Augmented Reality and More ETech Trends where she recalls with a great sense of humor that 2 years ago, augmented reality was only for labs and SciFi! She is also very active on Second Life. She mentions and share information about it a lot in the Second life matching section.

We like:
She created a whole set of iGoogle widgets in a single tab that will make your bioresearch easier. Visit Research tools iGoogle tabs to install it now.

Resources: http://etechlib.wordpress.com/

Twitter: @pfanderson

3. Alisha764’s Blog: A solo medical librarian’s ramblings

Who?
Alisha Miles graduated from FSU in 2008 with a Masters in Library Science and Information Studies. She is a solo medical librarian in non-profit hospital in Georgia. She created this blog to post ramblings about the medical library field.

What?
This new-yet-growing-famous blog (February 2009) is a nice place to read the fresh opinions and “ramblings of a young librarian. Among other things, you’ll be able to read quite a lot about Pubmed like this enthusiast post about its upcoming changes.

We like:
The extensive and well-argued post reviews she writes around new services she has been testing. One which is impressive and interesting to read is Google Health information: surprising facts.

Resources: http://alisha764.wordpress.com/

Twitter: @Alisha764

4. Eagle Dawg Blog: Perspectives in health informatics and medical librarianship



Who?
Eagle Dawg or Nicole S. Dettmar is a medical librarian at the National Network of Libraries of Medicine (NN/LM). Oh, and she is “not an acronym…(she is) a free woman.”

What?
Nicole is an extensive blogger woman who tries to cover what is hot in Medical & Libraries’ news and who takes part actively in discussions with her peers. She also dares to raise her voice to help through her community, like when she posted about the flood in the Louisville Free Public Library.

We like:
The Friday Foolery posts where she allows to talk about almost everything in a more simple way. She already goes by #52!

Resources: http://eagledawg.blogspot.com/

Twitter: @eagledawg

5. Krafty Librarian: Things of interest to a medical librarian.

Who?
Michelle Kraft is a medical librarian since 1998 and currently a medical librarian for a hospital system in Ohio. She is interested in technology and its outcomes in libraries.

What?
A lot of informative and technology oriented posts. For instance, she blogged recently about the Medical Apps and Phones. We lack some effort in design (or some personalization) however it helps reinforce the content over the rest. She is worried about explaining the trends in medical applications and how systems improve and change.

We like:
Her commitment when she went to the MLA conference and extensively blogged about it to keep her medical readers community updated on the news.

Resources: http://kraftylibrarian.com

Twitter: @krafty

6. The Search Principle blog: Dean Giustini on health libraries + web media



Who?
Dean Giustini is a reference librarian at the University of British Columbia at UBC’s Biomedical Branch Library located at the Vancouver General Hospital (VGH).

What?
Dean is a state-of-the-art social medias specialist and blogs a lot about it. The blog is a nice place to stay updated on the new tools medical librarians can use and on their applications in Canada.

We like:
Dean is a endless worker and shares tons of nice information on slideshare that will be very valuable to other medical librarians but not only.

Resources: http://blogs.ubc.ca/dean/

Twitter: @giustini

7. Women’s Health News: Women’s health news, politics, information, and resources from a medical librarian



Who?
Rachel Walden is a medical librarian with a degree in library and information science (MLIS) from the University of Pittsburgh, where she focused on medical librarianship and currently works in a prominent academic medical center library. She also works as an Editorial Assistant for the Journal of the Medical Library Association and handles clinical questions for medical center, including the diabetes clinic, impatient internal medicine, and the order set teams.

What?
She focuses on Women’s health News and is willing to provide information regarding current women’s health topics, including policy, legislation, news, and events, as well as to point readers to additional useful resources online. For instance you can read this post:How do you not know when you’re pregnant.

We like:
The blog posts by this medical librarian are more notes. They are most of the time short with a view to making it informative and straightforward. This is when the conversation begins with her community through the comments where she takes good care to answer them. Aditionnally, she proposes a list of useful health information you should be interested in if you’re into Women’s health.

Resources: http://womenshealthnews.wordpress.com/

Twitter: @rachel_w

8. Blog: Library of the Institute of Public Health



Who?
Ewa Dobrogowska is medical librarian from Cracow interested in Web & Medicine 2.0.

What?
She blogs in Polish but you will easily translates it to English (or other) through the Translate tool in teh sidebar. Plus you can follow her on twitter where she twitts almost exclusively in English which allows better interactions.

We like:
Her struggle to make Health information accessible on the internet and understandable by everyone.

Resources: http://www.bibliotekaizp.blogspot.com/

Twitter: @pudliszek

Edit: The two following librarians mentionned in this list (#9 & #10) are not medical librarians, nevertheless their work and blog posts appeared interesting enough to be listed here. We apologize for the lack of accuracy in the title and description.

9. The shifted librarians: Shifting libraries at the speed of byte

Who?
As she says:”My name is Jenny, and I’ll be your information maven today“. Jenny Levine is an internet Development Specialist & Strategy Guide at American Library Association. She is a highly skilled person in all emerging technologies and new tools and has already traveled across the US and Europe to give presentations.
By the way, what’s a shifted librarian? A “shifted librarian” is someone who is working to make libraries more portable.

What?
Her blog homepage is interesting as it consists of a daily stream displaying what she has been doing, reading, commenting and liking the past few days. You’ll have to click on the blog section to access the medical articles.

We like:
Jenny brings nice and educative resources as well as more distressed sections such as the gamin in libraries’ where you’ll find a set of posts about games (and mini golf) in a library!

Resources: http://theshiftedlibrarian.com

Twitter: @shifted

10. Musings about librarianship

Who?
Aaron Tay is a librarian at the social science departments of the National University of Singapore. Aaron is a librarian really into web2.0 who wants to keep track of interesting and cool ideas that might be used by libraries for benefit of users.

What?
The blog is really oriented to making the students’, professors’ and readers’ lives easier through the use of web2.0 tools. The posts aim to explaining in depth how to make the most out of them. For instance, the latest posts explain 8 ways to share links with users.

We like:
We like the top ranked post Subject guides on web 2.0 startup pages – 12 widgets! A must read.

Resources: http://musingsaboutlibrarianship.blogspot.com/

Twitter: @aarontay

And now our bonus medical librarian we highly recommend for the Spanish speaking people.

11. Biblioteca Médica Virtual

Who?
María García-Puente is responsible for the library of the Torrevieja Hospital (Spain)

What?
The blog’s objective is -according ot her saying- to make health science easy. She blogs regularly about the new services on the internet that make the medical librarian’s life easier. She also collaborates in congresses and recently made a bright presentation of how to get the most out of RSS feeds in the medical field.

We like:
The regular work she brings to her blog which has helped her become the reference for medical librarians. The fact that she is form Spain makes us like her even more.

Resources: http://bibliovirtual.wordpress.com/

Twitter: @bibliovirtual

We recommend you to read:

• Social media, web services and tips for health in MedLib’s Round 1.9
• Interview with Christian Blaschke, scientific director of novoseek
• How to create biomedical gadgets in a few steps
• A review of the main reference management softwares
• Call for MedLib’s Round 1.9 submissions