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Posts from the ‘Semantic Web’ Category

GoPubMed: Social Networking Features for Biomedical Experts

When I took a look at, my first reaction was “Wow”! Transinsight tells you what happens when you mix PubMed with semantic web.

Biomedical research happens in networks of researchers. Social networking web sites like FaceBook, LinkedIn and Xing use personal networks to establish contacts. On these sites, however, connections must be defined by the users themselves. For the first time, GoPubMed now completely and automatically extracts collaboration networks from millions of biomedical science publications.

For each concept in the selected semantic background knowledge, GoPubMed’s “Hot-Topic-View” shows the collaboration network between top authors in this field of research. Collaboration networks can now be experienced and visualized.

GoPubMed also now allows these networks to be searched for possible experts and collaboration partners, a feature which leads to tremendous time saving when searching for appropriate experts. This feature is especially important in a specialized scientific world where it is becoming more and more vital to set up temporary teams of highly specialized experts.


You really should give it a try!

A Google-Powered Gene Sequence Web Search Engine

Yesterday, David Rothman shared an interesting application with me. Query Gene is a Google-powered search engine with which you can combine text and gene sequence fragment web searches. What can you do if you have a sequence and you’d like to know whether this sequence has ever been associated with genetic diseases?

Query Gene is a web-based program that searches for information about genetic sequences on the web. It is distinctive because it is not limited to a single database, but instead captures genetic information on the entire Internet using Google. Query Gene works by taking a gene sequence in combination with other search terms, finds similar sequences using NCBI’s MegaBlast, retrieves the descriptions of those matching genes from NCBI’s Entrez Nucleotide database, and performs a series of Google searches using the combination of your original search terms and each gene description.


In their example, they inserted a nucleotide sequence and a search term (genetic disease associated with). This application identified the sequence as human hemoglobin beta and listed search results like sickle cell disease.

Isn’t it fantastic?

RSS and Firefox Add-ons in medicine

I’ve written several times about how you can use RSS in medicine. I’ve featured:

  • PubMed Save Search
  • Third-Party PubMed tools
  • Intelligent RSS
  • Tags, Google Alert and many more


But here is a new and extremely detailed video about what RSS is and how it is useful. RSS is just awesome! Kudos to the author! Now I have to go and create the RSS feeds of my Technorati pages.

Don’t miss today’s best post of the medical blogosphere, Firefox Add-ons for Molecular and Cell Biologists at Bitesize Bio.


10 future web trends including personalized medicine

Richard MacManus at Read/WriteWeb recently highlighted 10 future web trends to look out for over the next 10 years.

  1. semantic web
  2. artificial intelligence
  3. virtual worlds including Second Life
  4. mobile web
  5. attention economy
  6. web sites as web services
  7. online video / internet tv
  8. rich internet apps
  9. international web
  10. personalization


And after getting a lot of useful comments, he created an other list.

  1. Integration into everyday devices: health-monitoring bathroom?
  2. Hyperlocal
  3. Data retrievel/manipulation agents
  4. Read/Write/Request Web (a.k.a. a “living machine agent”)
  5. User-controlled, open Internet Identity
  6. New forms of Internet Interaction: “flexible OLED touch-screens, new visualisation technologies”
  7. Extended Reality: full sensory coupling with the virtual world
  8. Expert Systems
  9. Blog reading automatically input into our brain:

    In 10 years time, we won’t have to worry about RSS Readers at all – everything we need to know on a daily basis will be automatically input into our brains each morning while we’re eating our breakfast.

  10. Personalized Medicine:

this has been on the cards for some time, but in the not too distant future our medical details will be online and the networking aspects of the Internet will be utilized to improve the way medicine is prescribed. As a recent report noted: “Imagine this: you visit your clinician, undergo genetic testing, and then you are handed a miniature hard drive containing your personal genome sequence, which is subsequently uploaded onto publicly accessible databases.” See also the blog ScienceRoll.

Fantastic thoughts! If you’re interested in the future trends of personalized medicine, check out this category!

Related links:

WikiProfessional Alpha Testing: a wiki of web 3.0

I’ve already talked about, a semantic medical and scientific wiki. This is a new site (currently in alpha testing) on which you can create now your personalized free Internet Desktop. What does it mean?


You can upload information about you and your scientific work and there is a Knowlet Space as well:

Exploring concepts using the Knowlet Space gives the user a view on the relationships between concepts found in a huge number of scientific publications in just a glance. The Knowlet histogram displaying the concepts related to the source concepts can be adjusted to give different views on the literature. A view on the experts publishing on the concepts of concepts of interest is also easily accessible in the Knowlet Space.


As you see, we can filter the results by semantic groups (anatomy, disease, etc.), you can browse among your own publications; but as it contains a lot of bugs and has just a few terms to search for, it’s hard to tell why this will be useful and valuable to the scientific community. The is going to be the desktop for all the branch-wikis, like WikiProteins:

WikiProteins is a consortium initiative and is technically supported by the Open Progress Foundation and the company Knewco Inc. Wikiproteins functionality and content will be free to contributing scientists in perpetuity.

WikiProteins is in fact much broader than just a ‘proteomics’ oriented environment, although a main focus is on proteins and their role in biology and disease. Many other focused planned Wikis for Professionals will be developed but these will all operate on the same database system and will be fully interactive.


I’ve got three invitations to give away! Check out Scienceroll later for more information on this futuristic wiki!

7 Tips: How to track the information you need!

Recently, some of the researchers here in Debrecen have asked me how they could track the changes of their field of interest. Even in the field of medicine or science, it’s crucial to be up-to-date and to find methods/tools that can make your work easier and more comfortable. So here are some tips on how to track the information you need, how to be up-to-date in your field.

  • PubMed Save Search:

Most of the physicians and scientists I know, go back to PubMed time by time and search for the old terms to see whether there are new additions to the database. If you use the Save Search function, you can get your PubMed updates via e-mail or RSS. You don’t have to search again and again, just sit back and wait for the next letter containing the newest articles in your field. How? Create an NCBI account, make your regular search and click on the Save Search button:


Then edit the preferences, that’s all:


  • Third-Party PubMed tools:

I couldn’t come up with a better expression. These sites/tools are based on PubMed but try to open new ways in searching for different scientific/medical terms. For example, NextBio is a scientific data search engine with which you can use PubMed in a more dynamic way. The CureHunter provides interactive network graphs of related drugs, diseases and therapies. Or take a look at PubMed Reader, a free web-based research program for displaying PubMed / Medline search results on an individual basis. It means you can create your own up-to-date Medline and PubMed literature search.

David Rothman has a lot more!

Screenshot of CureHunter

  • Use RSS or webfeed!

If you have to track more and more papers and online journals, then you should start to use RSS. It’s the best and most comfortable way of getting the selected information automatically what means you can read the articles in one place. If you don’t believe me, just take a look at some of my interviews with famous bloggers and see how many blogs/journals they follow every day. How? All you need is a feed reader program (like or log in to your Bloglines, Google Reader or Netvibes account. Then open your favourite medical/scientific journal or blog and click on the feed icon:


Insert that link into your program; browser or online tool and you made it. Let the information come to you!

  • Use an even better RSS!

Alan at Science of the Invisible pointed out the features of Aide RSS, a new service which is actually a web 3.0 application.


The service filters the RSS noise by scoring each post by the number of comments it received, number of times it’s been tagged in, inbound links from a number of blog search engines, etc.

It will definitely improve your productivity and makes it even easier to track the content you like. For example, you can get only the good articles or the best ones of a blog or site via RSS, it depends on your decision.


  • Use tags!

Tags are one of the most important features of web 2.0. Tags help you how to find content absolutely relevant to your needs. If you want to track your field of interest like this, try If you’re a scientist or a physician, then your site is Connotea. Connotea can quickly save and organize links to your references, moreover you can follow the new additions to a tag by RSS. Here is the example: follow the best/selected articles about medicine 2.0.



I know BioWizard should be in the category of 3rd-party PubMed tools, but I think this service is much more than that. It keeps you up-to-date with the most important published literature as chosen by the global biomedical research community. How does it work?

BioWizard users submit relevant, timely research articles they have found to be useful and interesting. The articles you submit are then read by the rest of the community who promote articles they feel are deserving of recognition. The best articles in a research field are brought to the top page for all to read and discuss.


Through Biowizard, not just you can track all the papers writing in the field of yours, but you can get the best articles (selected by the scientific community) via e-mail.

  • Google Alert:

If none of these work for you, or you’d prefer an even simplier method, then use Google Alert. It will bring all the recent articles/blogposts to you, all the new results for your search term. Personally, I follow the term personalized medicine via this free service to know about all the new articles written on this topic.


As it’s so important to be up-to-date in your field, use these simple, free and comfortable methods to track the information you need. If you happen to know more tools/services, don’t hesitate to leave a comment for us.

Related links:

What’s on the web? (18 August 2007)


  • Wikipedia links in SwissProt (What You’re Doing Is Rather Desperate): Does it mean that Wikipedia is now an acceptable academic resource for biology?



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