Human and machine readable attribution

Whenever we post information on any electronic network, there are at least two audiences: human beings (typically viewing the information through a web browser) and automated agents (e.g. web crawlers). Until recently those who wished to inforrm these two audiences of any use restrictions or intellectual property had to do so twice: in machine readable form and in human readable form. One of the problems in having two forms is that with time (or even from the start) they may not represent the same restrictions or openness. That can lead to, at the very least, misunderstandings and annoyance. Fortunately, one of the more useful ways of the Semantic Web is how it allows for a flexible combination of representation that allows both audiences to be served in the same expression. Here is a particularly useful and recent example.


Collective editing of biological pathways

Following on the successful model of wikipedia a previously centrally managed biological pathways curation activity (e.g. genmapp) has now gone fully community based in the wikipathways project. This is an ambitious project at many levels. The least of the challenges is the technical, how to allow group editing of a connectivity graph? This has been implemented, quite successfully at first glance, by using a Java applet (i.e. called from within the browser). The greatest challenge will be of course a) getting a critical mass of annotators and b) getting collegiality among these collaborators without allow the religious wars that tend to break out over the smallest of disagreements of the appropriate way to represent knowledge. With regard to the former, I note that there already appears to be a community forming around the annotation of apoptosis pathways but when I searched for POMC, nothing was returned although I could find some of the receptors related to that peptide here.

So, it's up to us to make it successful or not. We'll see if the organizers of this resource have found the sweet spot for such a collaborative effort. Here's hoping they have.


Librarians and translational research: One year of accommodation

Given how central informatics is to the Harvard University CTSA proposal, the directors of the HMS Countway Library of Medicine (who also happen to be co-directors of the HMS Center for Biomedical Informatics) recently decided to help out with a challenging problem: Where to house the CTSA leadership (including Lee Nadler and Steve Freedman) until the University will have prepared their more permanent home next year? We (Alexa McCray and myself) offered to give up our offices on the fifth floor of the Library for one year and relocate ourselves on the fourth floor for that one year. Lee and Steve promised not to get too comfortable in our Library and Daniel Ennis of the administration assured us of the efforts made to create a home elsewhere for our CTSA colleagues.


Aging and the C-section

This study is a nice example of how we can track secular trends through publicly accreted data. As we have children later in life it may well be that we are running against some biological limits that Obstetric surgery allows us to overcome. As we instrument the healthcare enterprise using informatics technologies, more and more such testable hypotheses are going to be generated. Will we have the governance in place throughout our healthcare systems to test these hypotheses in a timely and responsible manner? Do we have the expertise and tools in place?