This impressive compilation from GOOD (the data issue) documents the impressive growth of Application Programming Interfaces that provide third party software developers with access to, and the ability to repurpose, large and very useful data sets. This growth is driven both by altruism and self-interest and represents a dramatic refutation of the skepticism towards the open data movement of merely a decade ago.
Hat tip David Kreda
This note from the American Medical Association nicely summarizes the recent approval of certification in Clinical Informatics by the American Board of Medical Specialties. It represent the closest encounter between clinical training and librarianship to date. We'll see what it portends for relative compensation.
Much has been written about the importance (or lack of it ) of happenstance in browsing through books on shelves and what we have lost with web-borne search. Thanks to Juliane Schneider, we are exploring how to augment the moment of serendipity using QR codes that students armed with a common "smart phone" can scan and thereby scoop up more information at a glance. Check out our 3rd floor for these codes printed on cards inserted in shelves. Paper chase now has web hints.
Billions of Google searches may seem to be evanescent, ephemeral, electronic abstractions but this article suggests that they leave a weighty, grimy residue. The company’s electrical consumption (mostly the data centers) is said to create a carbon footprint of one million five hundred thousand tons in a single year. That is possibly much less than the footprint left by the car/bus trips and phone calls that have been made unnecessary by web searches. But it does suggest that search engines that will be better (i.e provide the sought for answer in fewer searches) will also be greener, even without more efficient computational hardware.
This instance of the xkcd comic strip explains much of what is wrong with our current password systems and why, for example, the passwords protecting clinical information systems are hard to remember and easy to crack. Hat tip: Sam Volchenboum
Researchers in artificial intelligence (AI) of the 1980’s, librarians and aficionados of the Semantic Web have a shared faith: The unique value of human-designed knowledge structures whether they be taxonomies, ontologies or metadata. These knowledge representations are seen as providing important leverage in information retrieval, knowledge discovery, and decision-support. In this context, I was recently reminded by Alal Eran of an article by researchers at Google about the value of BIG data. These researchers (one of whom wrote a wonderful book on Common Lisp—Paradigms of Artificial Intelligence Programming: Case Studies in Common Lisp
For those of us in libraries and those of us who are librarians, there is now an active debate that has yet to achieve resolution on what value there is in human annotations and metadata. If there is value, at what cost? And if it is cost-effective, how do we demonstrate the efficacy? Our Universities' leaders will be interested in the answers and so will our colleagues at Google.
Recently, we held a summit on the topic of clinical grade reporting of full genomic sequence. Given the growth in the number of papers (likely to grow hyperexponentially in the near future) David Osterbur has followed up with a very nice bibliographic guide to this emerging literature. Feel free to contact him if you would like other such articles added to the guide.
This twitter feed of returns of items borrowed from the Countway Library provides a glimpse of the vibrant engagement of our community with the scholarship of the present and past. These include The Anatomy of madness : essays in the history of psychiatry, Calories don't count by Herman Taller, Tachycardias--mechanisms, diagnosis, treatment, and Observed brain dynamics by Partha Mitra. One could presume that these were not all borrowed by the same patron, but if they were, what questions were they asking?
That bird rendered by taxidermy in a museum is not only of visual interest. This report by an enterprising undergraduate points to some unexpected public health insights gleaned from the feathers of these museum specimens about the trajectory over centuries of mercury contamination in seabirds. Perhaps needless to say, this could not be done with a purely virtual collection.
A nice appreciation for National Librarian Week can be found here.
Hat tip: Daniel Masys
We are hosting a sobering exhibit about what happens when medical science loses its moral compass. More details can be found here.
A very creative approach to impactful scholarship. Worth the try even if if fails.
Hat tip: Christopher Erdmann
Do you think that you can create the new software app that will revolutionize healthcare? Do you agree that substitutability will allow us all to innovate healthcare practice? As detailed on the challenge.gov website, there is now a very short term opportunity to "walk the talk" for a modest prize and immodest glory.
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Is your desk topped by the monumental accreta of your work or does it retain it's pure sheen of Scandinavian simplicity? It turns out that the dichotomy between the "Neats" and the "Scruffies" cuts across several broad swathes of the human condition. Among these are the archane arts of taxonomization and representation so well known to librarians, botanists, and engineers working on electronic health record interoperability. On the latter topic, the President's Council of Advisors on Science and Technology, (PCAST) report has issued a report on how health information technology will or will not be effectively used to improve healthcare. Given the work we are pursuing on substitutability, our own Ben Adida shared a perspective on the report.
Kudos to the analysts at SCImago. They have provided an outstanding, entertaining and educational perspective on worldwide academic publishing. I'll focus here on only one aspect: citations. Although the United States is the leader in citations at 87M citations, it is a surprising laggard in self-citation (32% citations are self-citations). The leaders are China (62%), Lithuania (38%), and Iran (37%). However, in the domain of medicine, authors in the United States are considerably less reticent and rack up a self-citation rate of 47%, earning them second place. The map below of the subject areas of the USA publications indicates where the action is.
Hat tip: Peter Park
As Harvard University reorganizes its extensive library system, it is worth reconsidering where library activity occurs and who drives it. This effort in Finland (hat tip David Osterbur) is a reminder that although professionally trained librarians with a mission and institutional memory are central to the curation, preservation and dissemination of scholarly materials, there is no sharp demarcation as to where expertise, time and effort can be found in our collective efforts. If individual scholars do not curate their own, increasingly electronic, notes, their messages, and other residua of the scholarly process, there will be very little for institutional librarians to work wit and a gaping hole in the scholarly record. But first, academic institutions will have to provide them with a easy to use process that can last their entire careers. This is a first class opportunity for entrepreneurial, techno-librarians who can think at the scale of the Internet. Conversely, libraries must reach out the to network of distributed expertise in all areas of academic endeavors which is populated by experts often well outside the walls of organized academe. Literally tens of thousands of precious modern and ancient scholarly archives remain in the dark, queued up, waiting for an overworked archivist to provide even the most cursory cataloguing. Shotgun mass annotation, leveraging external expertise will have to become the norm and, again, there is a large opportunity for those who are able to provide such capabilities at scale and with the appropriate legal and institutional framework.
from a doctoral program in the life sciences is a reasonable goal, under most circumstances. For some unfortunates, it is not. Prospective students should make sure that they have the key bits of information required to decide if and where to proceed with a specific graduate program. If you are already in graduate school at Harvard University, you might want to consult with some of the faculty who are knowledgeable mentors.
We are getting very close to the point that genome-scale sequence is available for clinical use. But will we know how to process and interpret it for such clinical applications?
Harvard Medical School, Children’s Hospital Informatics Program, and Harvard Medical’s School Center for Biomedical Informatics, the Partners Center for Genetics and Genomics, and the Harvard Medical School Center for Computational Genetics will hold a working meeting on December 7th and 8th, 2010 at the Countway Library on the Harvard Medical School campus. The purpose of this meeting is to directly address the challenges of providing consistent and clinically useful information to physicians and their patients based on large-scale genome sequencing. This meeting will focus on developing a "pre-competitive space" where industry collaborates earlier and more often to accelerate the clinical benefit from next-generation sequencing. Attendees are from clinical laboratory, sequencing, electronic health record companies as well as governmental and academic groups. This is a free but limited attendance meeting so please contact me if you are interested.
A recent study exemplifies the leverage that can be obtained from mining existing, public data sets to further our national healthcare agenda. As described by the NY Times, our colleague John Brownstein obtained data from the Centers for Disease Control and Prevention (CDC) and U.S. Environmental Protection Agency (EPA) and found a consistent relationship between the amount of air pollution (particulate matter in the air) and population risk for diabetes (after correcting for the usual suspects such as income and ethnicity). This and other large-scale populations studies such as the one we recently reported by Atul Butte suggest that we might be insufficiently including the larger environment in our study of the diabetic plague that has afflicted us.
It also suggests that we have insufficiently taken advantage of freely available public data to pursue relevant and timely medical research.
