Knowledge beyond words

Use case: Is Low Vitamin D Levels Associated With Greater Risk of Relapse in Childhood Multiple Sclerosis?

Valentin — Mon, 14 Jun 2010 09:38:36 +0000

We have known for some time that vitamin D insufficiency is a risk factor for developing Multiple Sclerosis and we would like to know whether vitamin D levels influence the disease course of those who already have Multiple Slcerosis and what are the scientific articles dealing with the subject. This use case nis inspired by an article seen on ScienceDaily.

We first search for Low Vitamin D in novoseek. There are 8,916results in Pubmed and 3,714results in Free Full Text up to date.

We are interested in low Vitamin D Levels so we click on “Vitamin d” from the “Pharmacologicl Substances” category in sidebar to add it to the current search and make it more specific. We now have 4,584 results in Pubmed up to date.

Now, we need to look up for Multiple Sclerosis disease-related articles. In order to do so, we will check if it appears in the diseases category in the left sidebar. We need to click on the “more” link to see all the diseases related to the current search. Multiple Sclerosis diseases does not show up so we have to think of another search strategy.
The other way of searching for “multiple sclerosis”. It consists of typing in the search box: low vitamin d and “multiple sclerosis”. Typing the term “multiple sclerosis” between brackets will tell the system to look only for these two terms when they are mentioned together. We press search and we now have 61 results in Pubmed.

Note: in order to make the search even more specific and relevant, we can click on the “multiple sclerosis” filter that now appears at the top of the related concepts list in the Diseases category.

Last search term to be added to the current search consists of adding “children”. This will help us consult solely articles related to humans. You can either add and children in the search box or look in the sidebar where the category Organisms appears and add Homo Sapiens (showing up in 4th position) to the search. We now have 34 results in pubmed.

Those articles found in a few steps in Pubmed are satisfactory and help start working on knowing if Low Vitamin D Levels Associated With Greater Risk of Relapse in Childhood Multiple Sclerosis.

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Your handy my novoseek guide v1.0

Valentin — Mon, 24 May 2010 15:07:19 +0000

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:

Tip #4 to improve searches in novoseek: Create email alerts

Valentin — Tue, 11 May 2010 16:22:58 +0000

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.“).

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.

After saving the search, novoseek offers you to create an email alert for this very search. Click the “create alert” button.

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

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!

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A surprise for our fans on Facebook

Valentin — Wed, 28 Apr 2010 14:43:30 +0000

For more than one year, we have watched and learned from your search habits in order to deliver the best experience while searching for scientific articles. We have shared use cases, tips, resources, news, events, surprises and more on our blog. You can be sure that we will keep doing so! We’ve also been drawing your attention to our Facebook Like Page where we share valuable information, and news with our user community.

Today we’d like to thank these “fans” with a special update that might change their search experience for scientific articles forever. Drum rolls please…

In order to discover this surprise, you just have to “like” the novoseek’s Facebook Page once you are in the Surprise Tab and reload the page. For those who are already fan, enjoy the surprise!

What do you think of that?

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Earth Day 2010 – 10 relevant Open Access articles to read on that day

Valentin — Thu, 22 Apr 2010 16:46:19 +0000

The Earth Day turns 40 this year. These idea and movement started over a diner, and they have now become a global action day which concern everybody. The Earth Day is a great opportunity to get involved in making the world better. This is as simple as planting a tree, riding a bus instead of your car, taking your kids to Disney’s last movie Oceans, install solar panel on your roof get a convection oven or tracking your energy usage online… I am sure that you will find what to do today on this special day. Beyond one’s involvement for Earth Day, there is all the scientific efforts that are made to improve life on Earth and face the new challenges on Earth. We thought it would be a good idea to share with you 10 Open Access (Free Full Text) articles interesting to read on the Earth Day 2010.

Air Pollution: Salt Mist Is the Right Seasoning for Ozone. by Portera Carol in Environmental Health Perspectives
PMCID: 2453175
Room to Grow: Incentives Boost Energy-Efficient Homebuilding. by Schmidt, Charles W. on Environmental Health Perspectives
PMCID: 2199292
Terra Cognita: Using Earth Observing Systems to Understand Our World. by Schmidt, Charles W. on Environmental Health Perspectives
PMCID: 1277880
Cars, corporations, and commodities: Consequences for the social determinants of health by Woodcock, James and Alfred, Rachel in Emerging Themes in Epidemiology
PMCID: 2289830, DOI: 10.1186/1742-7622-5-4
Perchlorate: Health Effects and Technologies for Its Removal from Water Resources. by Srinivasan, Asha and Viraraghavan, Thiruvenkatachari in International Journal of Environmental Research and Public Health
PMCID: 2681191, DOI:10.3390/ijerph6041418
Indirect Potable Reuse: A Sustainable Water Supply Alternative. by Rodriguez, Clemencia; Van Buynder, Paul; Lugg, Richard; Blair, Palenque; Devine, Brian; Cook, Angus, and Weinstein, Philip; in International Journal of Environmental Research and Public Health
PMCID: 2672392, DOI: 10.3390/ijerph6031174
Population policies, programmes and the environment. by Speidel, J. Joseph; Weiss, Deborah C.; Ethelston, Sally A., and Gilbert, Sarah M. in Philosophical Transactions of the Royal Society B: Biological Sciences
PMCID: 2781834, DOI: 10.1098/rstb.2009.0162
The ecosystem-service chain and the biological spanersity crisis. by Mooney, Harold A. in Philosophical Transactions of the Royal Society B: Biological Sciences
PMCID: 2842713, DOI: 10.1098/rstb.2009.0223e
Environmental Remediation and Conversion of Carbon Dioxide (CO2) into Useful Green Products by Accelerated Carbonation Technology. by Lim, Mihee; Han, Gi-Chun; Ahn, Ji-Whan, and You, Kwang-Suk in International Journal of Environmental Research and Public Health
PMCID: 2819785, DOI: 10.3390/ijerph7010203
Is It Easy to Be Urban? Convergent Success in Urban Habitats among Lineages of a Widespread Native Ant. by Menke, Sean B.; Booth, Warren; Dunn, Robert R.; Schal, Coby; Vargo, Edward L., and Silverman, Jules 1 in PLoS ONE
PMCID: 2820551, DOI: 10.1371/journal.pone.0009194
Development of a biomechanical energy harvester. by Li, Qingguo; Naing, Veronica; Donelan, J Maxwell; in Journal of NeuroEngineering and Rehabilitation
PMCID: 2709631, DOI: 10.1186/1743-0003-6-22

These articles were found features of novoseek such as combinations of keywords, filters or advanced search. I also took good care to tag the articles in a “EarthDay” tag in my my novoseek account so I can retrieve them anytime as it is shown below.

Now tell us: What are your picks for 2010 Earth Day among novoseek’s Free Full Text articles? Share them with us!

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Interview with Christian Blaschke, scientific director of novoseek

Valentin — Fri, 16 Apr 2010 10:27:18 +0000

The interview of Christian Blaschke PhD, scientific director at novoseek was originaly published in Spanish and titled Bioinformatics in the business world in Jose María Fernández González’s blog. José María Fernández González is a bioinformatician at CNIO (Madrid – Spain). He has developed web services for iHOP. With a view to sharing it with the rest of the scientific community and english speaking people, we have translated it and published it here.

I’ve always wondered how to make a bioinformatics-related development in the business, because the objectives are different. In the scientific world almost always you have to publish prior to your competitors, whereas in the business world, the objectives are more related to the versatility and robustness of the tools and systems developed.

Therefore, when I got the opportunity to conduct a series of questions about someone who is “on the other side”, I grabbed the chance. Christian Blaschke, working at Bioalma answered my questions about the development of novoseek, a text-mining product.

Christian Blaschke is a graduate in Plant Physiology from the University of Salzburg and has a Ph.D. in Molecular Biology from the Autnoma University in Madrid. He began his career developing data-mining systems and information extraction in the Protein Design Group. Today he is the Research & Development Director and Principal Investigator in several European projects in which Bioalma takes part. He was also the coordinator for the first edition of the BioCreAtivE, an assessment for text-mining algorithms. He has been conducting research in text mining for more than 10 years.

In general, for ordinary people, what is novoseek?

It is a Web 2.0 search engine for scientific literature and also an alternative to Pubmed to search in Medline, in full-text articles from PubMedCentral and in U.S.
Grants. It is based on a unique text-mining technology that analyzes and processes the nearly 20 millions publications available in PubMed and the 3 million existing concepts in the literature. Our technology analyzes and takes into account the synonyms and homonyms to the search term, which allows to return relevant and complete results in the very first search. In addition, a profile (which appears in the left bar of the browser) is created for each search. This profile displays important concepts related to the search with a view to using them as filters and make the search more specific. Thus, the user finds the publications he needs to read in a more simple, fast and reliable way.

What was originally the idea to create this tool?

In the late 90s I was fortunate to work with Alfonso Valencia (then working at the National Center for Biotechnology in Madrid) in subjects dealing with word processing and information extraction. He was among the first to work on these subjects in the field of molecular biology and bioinformatics and I was able to explore many ideas. At that time we were interested in extracting proteins interactions and the analysis of the results on DNA microarrays based on the knowledge published in the scientific literature. Later we realized we could offer the benefits of the technologies we had developed to a wider audience and find a way in which biomedical researchers could benefit from it. So in Bioalma we started working on products that would be based on text analysis in the biomedical field. One could say that novoseek is the third generation of this products development and that we have now brought it online.

How many people were necessary for the development of novoseek? Did they / Do they have highly specialized profiles (text mining, databases, etc …)?

We started with a few people and we are currently a dozen that participate actively in the development of novoseek. We are a multidisciplinary team which includes people trained in many areas. From software engineers, experts in the development of databases, bioinformatitians, biochemists, pharmacists to experts in artificial intelligence. In addition we have long been dealing with texts and analyzing natural language. This is an area in which most of our team has experience.

Are there critical points with the current tools and web systems such as keeping the information updated and consistent. Did you have / Do you have many issues?

At first it wasn’t easy because the set of documents included in PubMed were much larger than anything we had processed before in our work experience. But I have to say that we have a great team and today we integrate documents published in PubMed (abstracts of publications) and PubMedCentral (full text) every day.

How do you get feedback from regular users? I mean, do they propose interesting features, or do they help you detect problems or system failures.

Novoseek is a service based on state-of-the-art technology, people working in the company are quite young, they know the internet well and are concerned with constantly improving the user experience. Therefore, their feedback is very important to us. We have opened discussion platforms that have a particular role. In uservoice, users tend to make us suggestions as to new developments and usability. We study them and we include them into our development “road map”. There are things that are easy to implement and take little time (like export to CiteULike) and others that we need to assess and may take longer (such as search in figures and images). Twitter (@novoseek) is a tool we use for real time communication with our users and to share information such as: interesting publications, news and interesting links for our community, surveys or a more direct feedback. For example, I remember the time someone asked us if novoseek was down and in 5 minutes, 5 people (including us) told her that it was not.

I admit that there is a subtle balance between what people want in the web-based service and what we think is good for efficient searches and a nice user experience. In general, user feedback helps us a lot.

If today you had to start from scratch the design of a tool with the same target as novoseek, having the background that you now have, what would you not do?

Our professional education is very technical and this was reflected in our previous products. They were very powerful but sometimes too complex for our target audience. We thought that more (functionality) was better than less and we did not consider enough the point of view of our users. For us this has been quite a journey in which we learned a lot. In the last months we have conducted many usability tests, and we realized that there are elements that are not clear enough. So we are currently working on a redesign of novoseek. This should help understand better how it differs from PubMed and what it actually bring to users.

In the current scientific landscape of web 2.0, web services, bibliographic social networks (such as CiteULike, Zotero 2.0, …), etc … that is beginning to be beyond PubMed or Google Scholar “Are you facing many challenges to link (or provide links) to these resources?

Given our work and activity online, we know well the other web 2.0 tools that today are part of the life of a novoseek user. They are tools we are also using ourselves and that we consider important because they are completing the service offered by novoseek. It is a requirement that we must meet so that people keep using novoseek. So far, we have done it for CiteULike and it is pending for Zotero 2.0 and Mendeley. As these web 2.0 services grow in number and their use is increasing among scientists, novoseek has to be more compatible with them.

Nearly all bioinformatics services today (either academic or commercial) offer programmatic APIs. What can you tell about yours?

For novoseek’s API we have used REST based on the XML standard because it is relatively simple to use and there are libraries for most programming languages available today.
As for the functionality it offers, we tried to bring most things that can be done in novoseek to the API. One can do searches based on words and biological concepts (like e.g. genes, diseases, drugs or chemicals) to retrieve documents. The documents offer all the entries included in novoseek and these can be used as a basis for new text mining services. It also offers the key concepts that are calculated for a search related to the documents returned and that characterize this set of documents.
Our main goal is to offer the possibility to integrate the functionality of novoseek on other platforms. For example to enrich the content of web pages or blogs. Furthermore, it is now very common to do ” mash-ups” between different systems to create something totally new. We wanted people to be able to use novoseek in new ways beyond what might occur to us. People interested can request an API Key in http://api.novoseek.com

What are the future plans for a tool like novoseek?

In the future we want to extract more and more information from the documents which are indexed in novoseek to allow ever more powerful searches. One problem is that e.g. in PubMed you can not search for a person. If you search for “John Smith” the system will return documents where the name refers to different people. Or in documents where “J Smith” appears as an author, you do not know if it belongs to “John Smith” or “Jeff Smith”. Another problem that requires a lot of work is to find specific information such as, e.g., what drugs treat a disease or what are the genetic causes of a disease. We want to solve these problems for our users to save them time spent searching and so that they could devote to actually reading the documents that are relevant to them.

Can you tell more about the infrastructure needed to provide this service?

At first we set up novoseek on a small cluster of Linux machines installed in our offices in Madrid. But we realized that keeping a 24 hour service with minimum disruption was not easy. We were depending on a single Internet line that failed several times in the first months. The air conditioning system was not secure enough and we could not withstand power outages of over 15 minutes. After evaluating many options such as hosting of machines in a data center or collocation of our own hardware in one of them, we chose the web services offered by Amazon (which is known as AWS – Amazon Web Services consisting of EC2 and S3). Amazon offers what is known today as “the cloud”, a system of virtual machines that are configured in a flexible way. It is easy to create more nodes to meet our growing needs and also pay only what is actually used. The decision to migrate novoseek to the Amazon platform solved the problems I mentioned before because it is a very stable environment that has not failed us so far.

Thank you to José María Fernández González and Christian Blaschke for their time and dedication for this interview.

You can get an API key here

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World Health Day to encourage healthy habits in cities and urbanizations

Valentin — Wed, 07 Apr 2010 16:00:28 +0000

Today April 7th 2010 starts the World Health Day, organized by the World Health Organization. Its goal has been, for more than 50 years now to spread the “awareness of a specific health theme to highlight a priority area of concern for the World Health Organization (WHO)“. The theme of this year is “1000 Cities, 1000 Lives” to show how cities and people are able to encourage and develop healthy behaviours through their communities. You can already explore who is joining the global movement to make cities healthier on 1,000 cities, 1,000 lives website but also join the movement, create your own group of healthy activities, post photos and videos… The World Health Day is a great opportunity to go outside and share your healthy habits!

As this year the World Health Organization wants to emphasize healthy habits in cities, we have performed a few searches on novoseek to dig the scientific literature in order to find what has been written on this subject. This will also allow you to see how to perform effective searches in a few clicks. Indeed, in the scientific literature, there are a great deal of articles mentioning World Health Days (168 articles in Pubmed and 20 Free Full Text articles to date).

To perform the first search, we go to the Advanced Search panel and enter the following keywords for in the corresponding fields: healthy habits, city, cities.

This search yields interesting results about healthy habits in cities in Pubmed such as the effort of Louisville for incorporating active living principles into planning and design. This very search in Free FullText articles yields very interesting results as well. For example, we recommend you to read this fulltext article dealing with Physical activity as a preventive measure against overweight, obesity, infections, allergies and cardiovascular disease risk factors in adolescents: AFINOS Study protocol.

Do you feel like sharing your healthy habits-related readings and behaviours with us? What are you doing to encourage the World Health Day spread his message?

Tip #3 to improve searches in novoseek – use labels to organize your readings

Valentin — Wed, 31 Mar 2010 16:19:27 +0000

Users of my novoseek enjoy more features than the average user on novoseek. Those features allow to perform important tasks when one is searching for relevant biomedical information online. Indeed, every person (researcher, medical doctor, medical librarian, student or just interested in life sciences) is willing to make the searching process a nice experience and time-effective task. So far, novoseek allows to check search history, save searches, create email alerts and label documents. We are going to show how to label documents thanks to the option available in my novoseek.

What’s a label? A label is a descriptive term that is used to classify documents. In novoseek, you create the labels you want to assign to documents you need to read, print, share… and you organize your own library of biomedical articles.

Sign in to my novoseek. If you haven’t registered yet, feel free to sign up for a free account now.
Perform a search in your area of interest. For this example, we have performed a search for coriza, the scientific name for common cold.
Select the article(s) you want to assign a label to (to do so you just need to check the tiny box at the left of the article’s title)
Click on Labels in the interface tool bar and:
- Click on the Label you want to assign to the selected publication
- or Create a Label
We encourage you to create labels such as “print”, “read” and “share” to start organizing the scientific articles and be better organized. Other create labels according to the subject they are investigating. There are no limits to creating and using the Labels in your daily tasks.
Now you can see which articles have Labels

You can also assign a Label to a document from the very document page

You can assign several labels to one single article

You can access your labels and the publications you have assigned them from my novoseek. The overview panel lets you consult basic information on labelled documents whereas the Labels category lets you consult the documents assigned per Label, edit them and or delete them

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

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House M.D. shares his scientific secrets

Valentin — Wed, 31 Mar 2010 07:36:43 +0000

Everyone knows Hugh Laurie as the brilliant, pill-popping physician Dr. Gregory House on the Fox TV series House M.D., a role that’s brought him Hollywood superstardom, three Emmy nominations, two Golden Globes, and an estimated $400,000 per episode.

We are huge fans of this medical investigation drama, which is about to enter its fifth series, featuring its 100th episode. It was an incredibly refreshing surprise when we found this interview from Entertainment Weekly’s March issue, where “Dr. House” was asked how he prepares for his role?

Hugh Laurie stated, “I tried to get some time in American hospitals but the whole thing happened so fast that I ended up just having to fake it. That’s what actors do after all! But when the script for the next episode is handed to me, I get some scientific research done with a search engine called Novoseek so I can know what I’m talking about. It’s pretty useful since we have to learn all kinds of very detailed medical terms and descriptions”.

Isn’t this amazing?!!!! Dr. House uses novoseek! the interview published in Entertainment Weekly is shown below.

PS: April Fool’s!

Improvements in novoseek – March 2010

Valentin — Fri, 26 Mar 2010 15:38:47 +0000

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!

Knowledge beyond words

Use case: Is Low Vitamin D Levels Associated With Greater Risk of Relapse in Childhood Multiple Sclerosis?

We recommend you to read:

Your handy my novoseek guide v1.0

We recommend you to read:

Tip #4 to improve searches in novoseek: Create email alerts

We recommend you to read:

A surprise for our fans on Facebook

We recommend you to read:

Earth Day 2010 – 10 relevant Open Access articles to read on that day

We recommend you to read:

Interview with Christian Blaschke, scientific director of novoseek

We recommend you to read:

World Health Day to encourage healthy habits in cities and urbanizations

Most Commented Posts

Tip #3 to improve searches in novoseek – use labels to organize your readings

We recommend you to read:

House M.D. shares his scientific secrets

Most Commented Posts

Improvements in novoseek – March 2010

We recommend you to read: