Entries from June 2009 ↓

From novoseek, the team is trying hard to deliver a quality service and make our biomedical search engine an intuitive and easy to use one as well as powerful. Every now and then we have the opportunity to help someone with a search that results a bit difficult.

Today we’ve had the chance to catch a bribe of conversation on twitter where a medical doctor was wondering if anyone knew about Asperger Syndrome and Bipolar disorder in people affected by autism. We took the opportunity to suggest him a set of results and as he was satisfied, we are bringing it to you here so you can know how to perform an effective search with novoseek, your new biomedical search engine.

A good way to look for publications about asperger syndrome and bipolar disorder in autism is to start with autism from the main search box. The results page for autism displays 10.633 publications in Medline. We should use the related concepts in the left sidebar to refine the search. As they are classified by relevance to the current search and by concept, we should be able to identify what we need quickly.

Since Aperger syndrome is a disease, I have to click on the more link just next to disease in the left column. This allows to see all the diseases related to the current search for autism. In this case the seventh one is Asperger syndrome. I can click the iicon and chose Add filter or click directly on it to add it to the current search. We now have 681 results in Medline.

I am going to repeat the process with bipolar disorder. This one is almost at the bottom of the list.We now have 12 results in Medline for the search on Asperger syndrome and bipolar disorder in autism. According to them, the medical librarian was satisfied. It could be a good start to study in this field.

By default, documents are sorted by date (newest first) and document details are shown with snippets but you can sort them by relevance and chose to see more of every publication. Just click the icons and chose to see the title, sentences or the complete abstract.

Any suggestion or question, feel free to ask us directly by commenting on the post or through our platform on uservoice

Some days ago, we finished the migration of our production site to the Cloud, more precisely to Amazon EC2. I do not know if the “Cloud Computing” needs defining, but in any case I invite you to watch this wonderful video made by the people of Salesforce.com, in which you can find an easy and intuitive definition of Cloud Computing, and a list of its benefits.

What benefits does provide the Cloud to a search engine like novo|seek offer? I am probably going to repeat most of the same arguments listed in the video, anyhow:

• Cost reduction: in the Cloud we pay for what we use: CPU time, storage, bandwidth…
• Easy scaling: for a growing search engine like novo|seek, scalability is critical. For us, the user experience is very important and thus the QoS (Quality of Service).  Dimensioning the servers of an emerging web site is a hard task. If you get short, any marketing or PR action that drives a lot of traffic to the site can get the servers down on their knees.  On the contrary, if you over-dimension your infrastructures, you will have your servers getting old inside your data center. Amazon EC2 let us re-dimension our production infrastructure at the same time our traffic grows.
• Reduction of the Time-to-market and the entry barriers to innovation: The EC2 infrastructure lets us create new server instances fast and easily  with different sizes and performance. If we need to try new text mining algorithms or expand our technology to new data sources, the Cloud will allow us to instantiate all the required servers to meet our extra computing power and we can forget about finding new room in our crowded data center. Cloud computing lowers the innovation entry barriers to small and medium size companies like us.

We know that we are not the only Company in the sector to take advantage of Cloud Computing, BioTeam, for example, is adapting bioinformatics solutions so it can be run in Amazon EC2.

Not only small and medium companies are in The Cloud, big pharmas like Jonhson&Johnson or Lilly, are developing their first projects on EC2 although a recent report from McKinsey stated that Cloud Computing will not reduce costs to large corporations.

The novo|seek team is sure that moving to The Cloud will improve the quality of the service that we are currently providing, and will let us bring to all of you the innovative features cooking right know at our R&D department.

Greetings from the cloud!

Microsoft has long been striving to be someone in the search engines landscape. Unfortunately, they have never achieved it. But on May of 2009, Microsoft stroke again. They released Bing, a new search engine with over 100 millions budget which should be enough to make it a great competitor on the market. So we’ve put it at a test. Is Bing that Big? What does it have to offer? Is it worth using it for searching biomedical literature?

Is Bing that big? This is what we’ve wondered after it’s been released and all the discussions there have been around. As we are concerned by delivering useful resources for the life sciences professionals, we decided to put Bing a test for biomedical research.

What biomedical information this search engine can give you? We started with a very basic search on Breast Cancer. First of all, the amount of results is huge. No less than 50.300.000 results for this mere search. Mainly because there are so many results, you have to get used to it before you can analyze where to find the information you need to read. Obviously the main results, the ones you are used to have in every search engine are displayed in the center, below the search box and premium advertising. There is one thing that is funny with Bing, they didn’t beat around the bush and put the information in the same way as google does (blue titles, black text and green URLs). Who knows, they could be right after all.

Once you are used to the layout of the page you can start analyzing how is the information clustered the way we show it to you below.

1. Features the main search result meant to be the most relevant. This result often mentions the Wikipedia result as google does.
2. When available, Bing displays a set of related informations to the query you’ve typed in, like Articles, Symptoms, Treatment, Stages, Surgery, Prevention and Reference. This is an interesting feature but unfortunately it does work only for really general queries such as Breast Cancer. Try Breast Carcinoma (synonym of breast cancer) and you won’t get any related information in that way.
3. Displays relevant Related searches to the current search. Don’t expect to have anything very specific though, the related searches are general. That is to say, the last 2 related searches suggest Lung and Prostate Cancer.The same search in novoseek would allow you to refine it with more specific breast cancer-related filters such as invasive breast cancer, brca2 mutation or contralateral breast cancer…
   
4. Search history. Nice functionality and very simple to use. You can turn it off whenever you want or just go to your search history and clear some of them, if you need to.

Now let’s keep reviewing Bing a bit more. As you scroll down the results you see the information clustered in the categories we mentioned before. If you click on them, you will have the whole set of results in that field. This is an interesting feature but unfortunately it is hardly working.

One of the interesting thing that Bing is doing is the preview of results as shown in the image below. It will help you read more of the article without having to click on it. It is not yet revolutionary but still it is interesting to consider as an additional function.



After this sample search, it seems clear that we are not dealing with the same amount of information and ways of treating it as would a biomedical search engine would do. To be true, BING does not propose much compared to Google but it still has this brand-new-product effect. The technology is not yet an outstanding one. What is true is that the results are pretty similar to Google or Yahoo. So Bing may not be that big but it could compete with Yahoo who is still late in bringing innovation on the market.

Last but not least. How hard for Microsoft Bing to realize that when they are just launching their product, Google is giving a preview of Google Wave (web of the future?) and announces the beta release of Google Squared, another way of searching the web. It seems that whatever competitors do, Google is always a step ahead.

Is it necessary to present Wolfram Alpha, the new online research tool everybody is talking about those days? Obviously not! This is why we prefer to express our thoughts on it in 5 cons and 5 pros about Wolfram Alpha

5 cons on Wolfram Alpha

1. Wolfram Alpha is not a search engine but a Computational Knowledge engine. What in earth does this stand for?

Easy: Wolfram Alpha is not able to perform searches in an easy way. You have to put search terms with the right and correct words!

2. What kind of information is available in Wolfram Alpha?

Not a lot. Alpha is very specific. The best you can look for is mathematics, chemical compounds, dates, units or even the temperature in Madrid…Don’t get disappointed, we’ve warned you.

3. Wolfram Alpha is not clever on the contrary to what it claims to be

Information retrieval is based on a semantics and words tagging. With Alpha, if a word has not yet been tagged for one of its meanings in a context, you won’t get anything of it. What a pity! For example, try to ask it “Who discovered polonium?. It is not able to answer, while in google the same question is easily answered.

4. Wolfram Alpha is for hype people!

I mean, who is going to ask “How many roads must a man walk down before you can call him a man?” in order to have this result mentioning Bob Dylan. What if we ask “Who is Luke’s father?“, well, here goes the answer namely not much.

5. Wolfram Alpha is not a resource for biomedical information.

Despite what you’ve heard about it, Alpha doesn’t provide life science publications as novoseek does.

5 Pros on Wolfram Alpha

1. Wolfram Alpha, this is not a search engine! It’s better.

The way information is treated and presented is far from what you’ve seen and experienced until now. It is not Google nor Wikipedia. It is able to “computate” almost anything you ask it. Try solve a x^2 + b x + c = 0 for x

2. Wolfram Alpha could revolutionize learning and searching on the internet

Although it takes much to learn how to use it and obtain effective results, it could be an interesting tool for pupils, students and professors.

3. Wolfram Alpha has some surprises and easter eggs for you to discover.

Here goes the top 10 easter eggs in wolfram alpha. There may be more, it’s up to you to look for them.

4. The Wolfram Alpha team is working hard to keep it updated.

If there are some failures, be patient and for sure they’ll be fixed soon. The “Give us your feedback” box at the bottom of pages is there for you to point out these.

5. They are working on making Wolfram Alpha more user friendly

According to statements, they will release an API and more detailed search boxes in order to make searches easier.

Obviously, search engines on the internet are bringing changes and new ways of accessing information. Is this another step towards web 3.0 ?