Tuesday, December 23, 2008

The discovery of more knowledge (in repositories, research web sites, blogs, and the like)

In my previous post I was announcing the knowledge discovery 'button' that could be used to enhance any repository, science blog, or any researcher's, scientific society's, or publisher's site for that matter. Well, it is here now. Available to all. Incorporation of a small bit of code will equip any site who wants it with the knowledge discovery 'button' as you have it on this blog in the upper right hand side (the orange one that says "discover more..."). And with all the functionality that comes with it, of course. Even more functionality is being developed.

It really is a small bit of code that needs to be incorporated, and the fact that I managed to do it myself in this blog should give confidence to even the least HTML-savvy person that it really is easy. This is the code:
<script type="text/javascript" src="http://conceptweblinker.wikiprofessional.org/wikibutton.js"></script>
Just cut and paste it in the code of your repository, web site or blog and enhance its ability to serve up relevant additional knowledge to its readers.

As an example of what it might look like, click the "Discover more..." button and then look at this abstract of an article by Matsuda et al., entitled Silencing of caspase-8 and caspase-3 by RNA interference prevents vascular endothelial cell injury in mice with endotoxic shock. (Cardiovascular Research 2007 76(1):132-140;
OBJECTIVES: Septic shock and sequential multiple organ failure remain the cause of death in septic patients. Vascular endothelial cell apoptosis may play a role in the pathogenesis of the septic syndrome. Caspase-8 is presumed to be the apex of the death receptor-mediated apoptosis pathway, whereas caspase-3 belongs to the "effector" protease in the apoptosis cascade. Synthetic small interfering RNAs (siRNAs) specifically suppress gene expression by RNA interference. Therefore, we evaluated the therapeutic efficacy of caspase-8/caspase-3 siRNAs in a murine model of polymicrobial endotoxic shock. METHODS: Polymicrobial endotoxic shock was induced by cecal ligation and puncture (CLP) in BALB/c mice. In vivo delivery of siRNAs was performed by using a transfection reagent (Lipofectamine 2000) at 10 h after CLP. As a negative control, animals received non-sense (scrambled) siRNA. RESULTS: Marked increases in caspase-8 and caspase-3 protein expression in CLP aortic tissues were strongly suppressed by treatment with caspase-8/caspase-3 siRNAs. This siRNA treatment prevented DNA ladder formation and less phosphorylation of the pro-apoptotic protein Bad seen in CLP aortic tissues. Transferase-mediated dUTP nick end labeling (TUNEL) revealed that the appearance of apoptosis in aortic endothelium after CLP was eliminated by this siRNA treatment. Although all of the control animals subjected to CLP died within 2 days, administration of caspase-8/caspase-3 siRNAs indefinitely (>7 days) improved the survival of CLP mice. CONCLUSIONS: Gene silencing of caspase-8 and caspase-3 with siRNAs provided profound protection against polymicrobial endotoxic shock. The prevention of vascular endothelial cell apoptosis appears to be, at least in part, responsible for their beneficial effects in endotoxic shock.
If you click on any of the highlighted concepts (the colours disappear after a few seconds, so that you can read the text more easily, but they can be brought back by mousing over the button), you will get a number of options to explore further. First of all, 'add to search', which automatically extends the search argument with synonyms of the concept in question. For instance, if I search further in this way with RNA interference the search is automatically reformulated as "RNA Interference" OR "Post-Transcriptional Gene Silencing" OR "Posttranscriptional Gene Silencings" OR "RNA Silencing" OR "RNA Silencings" OR "Quelling" OR "RNAi" OR "cosuppression" OR "Sequence-Specific Posttranscriptional Gene Silencing".

The options of 'related authors' and 'related publications' are self-explanatory, I guess, and the option 'connected concepts' leads you to a page on which you find concepts that are connected to the concept you clicked on in one of three ways:
  1. there is a factual connection – established in a process of curation, e.g. via the peer-reviewed literature or a curated database such as SwissProt;
  2. there is a co-occurrence in the same sentence in the peer-reviewed literature; and
  3. even though 1. or 2. don't apply, there is such an overlap in the connections that each of two concepts have, that there is a strong 'predictive' association between them, strong enough to 'invite' research to establish if the concepts are indeed factually connected.
Each factual and co-occurrence connection has an 'explain' option with links to the literature from which the connections were 'mined', and so to further discovery possibilities.

There are also links to relevant books, and even more is in the pipeline.

Go forth and multiply (the use of this button)!

Jan Velterop

Tuesday, December 02, 2008

Repositioning repositories

There are more and more repositories and their significance for open access as well as for the universities and institutions that operate them grows, too. Yet many repositories have fairly basic functionality. Some don't mind, and see repositories as a way merely to provide open access or to archive the institution's output. This is a pity. Repositioning them, making repositories attractive places to come to for researchers – and to come back to – would greatly help in their potential success. Many are already on that track. And various developers of repository software, such as MIT's DSpace, are already in the process of starting to experiment with embedding technology that helps the discovery of more knowledge by making it possible for repositories to become 'portals' of sorts.

It's easy enough. Have a look at the functionality that can soon be added to any repository (or blog, or personal site, for that matter) and click the 'button' on the upper right hand side of this page that gives you the opportunity to discover more knowledge. Within weeks we hope to make the code for that button publicly and freely available, for anybody to use on any site (watch this space!). And even more functionality is being worked on and in the pipeline. For now, this technology allows you especially to discover knowledge in the main 'domain of its experience', the biomedical areas.

Below, I am listing a few of the more than a million terms that are recognised as concepts and when you click on them, they open up a 'balloon' with links to more knowledge. I'm just doing that because in this blog you may otherwise not really find too many scientific concepts.

But look at these: hepatic stellate cell – immunoreactivity – squamous cell carcinoma – nonhomologous DNA end joining – monoamine oxidase type B (MAOB) – nuclear envelope – rough endoplasmic reticulum – Kupffer cells – plasma membrane – Ku70.

The first thing you can do is search further. The search will automatically include synonyms. Even something simple as skin is, when used to search further, automatically expanded into the search argument: "Skin" OR "Integument" OR "cutaneous tissue" OR "skin system" OR "Integumental system".

But you can also see authors and publications that are specifically related to the concept you're looking at. And you can see what all the other concepts are that are connected to this concept, and how they are connected. All connections are explained, and these explanations have links to the original source from which the connections were 'mined'.

Of course, this is just the beginning. More knowledge and information that is permanent and relevant can – and will – be added in these balloons. If there is anything you would like us to consider to add, please feel free to give feedback. We do like to hear from you! (Use the 'comments' link below or the email address in the top of this blog.)

Jan Velterop