BLAST this!

David Osterbur often gives extremely well received lectures on the use of public bioinformatics resources for biologists. However, even he is limited in how many audiences he can reach. So, if you know of a biologist who needs some help in the use of BLAST, or the UCSC Genome Browser or even in the search of information regarding herbs and dietary supplements, you will be happy to know that the Countway Library (in collaboration with the MIT Engineering and Sciences Libraries) has made available several instructional videos. Let me know if these are helpful and if you'd like to see more (and about what).

Out of date but not dated?

This is a great example of how the instant-at-hand-reflexive-cut-and-paste nature of electronic information can bridge the virtual to inflict real harm. Contemplate how clinical out-of-date information can be similarly used to boost the medical malpractice of the incidentalome. Will medical libraries step up to the challenge of keeping the medical profession up to date?

[Thanks to Ben Reis for the pointer]

The Harvard Catalyst site is live and open

The name of the Harvard University Clinical and Translational Science Center is Catalyst. Several of its resources are publicly available. For example, you can now see the biomedical scholarly output of our university at a glance. You can find people, buildings, phone numbers, directions and parking across the entire University (!) with 18+ participating institutions. You can see the influenza risk across our local geography and recent history. You can explore which clinical trials are supported by the institutions across Catalyst. You can use Webdash to share web pages and publications and their citations with collaborators and colleagues. You can browse and search the available Core facilities (in the hundreds). And if you need analytic help you can reach out to the Catalyst biostatistics program and genetics program, for example. Within a year, we will reveal the data sharing function called SHRINE which allows authorized users to study patient populations (with regulatory oversight) for pharmacovigilance, and various clinical research projects (e.g genome-wide studies of asthma, major depression resistant to standard antidepressants).

This site is the collaborative effort of multiple informatics groups in our community, including HMS Center for Biomedical Informatics, HMS IT, and the IT groups of Partners Healthcare Systems, Beth Israel Deaconess Medical Center, and Children's Hospital. It was an impressive 107 day dash bringing together diverse applications into one package. It's still rough and in progress and I would welcome your comments as would our Research Navigators.

Just some cocktail party conversation for you: Note the relative decline of protein research (relative to other topics) in the past decade at our University. The same indicators (gratifyingly) show the rise of mathematical topics in our life sciences scholarly output. Our most prolific author is Walt Willet (note the alternate ways his name appears each with its own publication history: to be fixed in the next iteration of Medvane). Note that JBC appears to be a popular journal for our authors to publish in.

Information disclosure makes the case for information altruists

This just-published article in PLoS Genetics by David Craig and Nils Homer reveals how the straightforward use of information technology puts the identify and health risks of individuals within the access of the public if two conditions are fulfilled: 1) Their genome-wide data (e.g. from a SNP chip) was published online and 2) Someone has some DNA from that individual (e.g. life insurance company? Forensic experts?). This is essentially the genomic equivalent of the disclosure mechanisms that Latanya Sweeney highlighted in the case of conventional medical data. As a result of this article, several national research organizations, private and public, are now pulling data down from their websites. This is going to therefore result in at least a temporary setback in genomic data dissemination for research purposes. Which is going to sadden all of us who are working to bring biomedicine forward into the 21st century. In this context, it seems that we will really have to find large cohorts of health information altruists who are willing to share their data with full understanding of the risks, and perhaps full legislative protection against such risks.

Does electronic publishing diminish the breadth of the scientist's scholarly attention span?

In this article in Science Magazine (sorry, subscription required), Dr. Evans argues that it does. By reviewing citation data covering over 50 million articles going back to 1945, he presents evidence that the more a journal makes it's backfiles available electronically, the less the author of a manuscript is likely to cite papers that are further in the past and/or less closely relevant to her research. There are several dissenting voices with regard to this analysis, but let's ponder what it might mean. Dr. Evans suggests one cause may be the relatively poor pre-electronic indexing which compelled readers of print articles to necessarily cast a broader net while browsing the literature. A less charitable hypothesis would be that in the face of an overwhelming number of relevant articles, a prospective author will find enough relevant articles to cite within the most recent published segment of the bibliome and/or the most high profile journals. When enough authors follow this trend (perhaps by following the the citation styles within the most cited articles), the result is a general narrowing of scope of attention of the scientific community within each discipline, both in subject matter and in time. A more optimistic view is that we have all become more agile in our use of electronic search and that in the face of a mountain of less relevant publications, we have become much better at winnowing out the chaff. Or it could be that the ordering of search results by year could be biasing investigators (sorry, subscription required) in ways that they are not aware of. Regardless of the cause, in an era in which we have all called for "evidence based medicine," it should give us pause if our view of evidence is overly myopic due to its electronic immediacy and organization.

More genetics in high school than medical school?

This highly amusing story about fish that are not what they are said to be, should be a sobering wake-up call to medical schools. Here we read about students using third parties to DNA sequence and then taxonomize samples they procured in restaurants and groceries. In the article we read of high-school students (who are not necessarily interested in careers in science) whose scientific literacy with regard to genetics would put many physicians to shame. Admittedly, these students have privileged access to well-informed thought leaders and yet can we point to equally creative and hands on teaching of genetics (and its commoditization) in our elite medical schools? The gap between the public's knowledge of genetics and that of the "professionals" appears to be continually narrowing even while public expectations of the value of such knowledge continues to grow.

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?

Redefinition of community standards through evidence

This article in the NY Times (free registration required) reports on how Google is planning to use the frequency of search terms in various US communities to show that those previously defined as being outside the community standard are in fact more frequently used than "apple pie". On the one hand, this trend is likely to grow and may likely do so even in medicine (to define the standard of care from the data rather than from the experts interpreting the data). On the other hand, just because the majority follows a particular practice does not make it best, optimal, desirable or even necessarily permissible. It does however, shed considerable light on double standards of various stripes.

Blogosphere mapped!

This map of the blogosphere reveals both the political lay of the very densely populated land of blogs and the degrees of authoritativeness that each blog appears to hold. Where is the equivalent for the medical bibliome?

Pubmed central compliance trends

Just heard some very positive news from David Lipman at the NCBI. It does seem that investigators are responding very positively to the new mandate. Just in the last month, author submissions to Pubmed Central (PMC) have increased by at least a factor of five. The author-contributed manuscripts now exceed the journal contributed manuscripts. It also appears that at least 60% of the expected manuscripts are being submitted to PMC. NIH appears to be well on the way to capturing the vast majority of the published output of NIH-funded science which is a wonderful result for the scientific community and the public which it serves.

Harvard CTSC

As announced, Harvard University has been awarded a Clinical Translational Science Award. The Informatics Program is one of 10 programs in the Harvard CTSA and represents a trans-University collaboration whose initial plans are described here.

Important leadership for Harvard in open access publishing

Stuart Shieber, a professor of computer science at the Faculty of Arts and Sciences (FAS) has now assumed the leadership of the new Office for Scholarly Communication. This is the natural outgrowth of his leadership of the Provost’s Committee on Scholarly Communication and in making the case for Open Access publishing adoption at the FAS.

Meta-data strikes back?

Ben Adida writes in his blog about a very interesting development in the Yahoo search infrastructure. The bottom-line is that by opening up some of the search results processing through metadata-level (i.e. rdf) processing, Yahoo has enabled a much more personalized user experience. Now, we'll see if the developer community runs with this opportunity.

A skeptical view of electronic health record benefits

This report from the Congressional Budget Office (CBO) was widely reported in the press today. The press has mainly focused on the report's skepticism about earlier estimates of greater than $40 billion/year savings from broad national electronic health record adoption. This certainly is going to remain a point of controversy but other questions raised by the report merit broader debate. Do EHR's reduce duplicate ordering of tests and reduce adverse events in the outpatient setting? It has been my own intuition that it does, but this CBO report points out some contrary evidence. It seems that these questions constitute a useful research agenda for the medical informatics community which should be further pursued, in many healthcare delivery settings.

Genetic discrimination is a crime

The Genetic Information Non-Discrimination Act (GINA) was signed into law by President Bush. This is an important first step in moving towards making disclosure of genetic information no more (and no less) concerning than disclosure of medical and family history. All in all a positive step for harnessing the clinical fruit of the genomic revolution.

Get yourself or your post-doc in the 21st century.

For those of you engaged in genome-scale studies but not completely up to speed in Bioconductor and R. This very short course will be "conducted" by one of the leaders of the Bioconductor project (Vince Carey). Thanks to Vince, this short course is free of charge but you do have to register.

Title:
Statistical computing for genome-scale biology:
An introduction to R and Bioconductor 2.2
When: 27 and 29 May from 1230pm to 3pm.
Countway Medical Library: 4th floor
This course is intended to acquaint biologists and bioinformaticians with principles and methods of computing with genome-scale experimental data using Bioconductor 2.2. Registered students will have access to media for installing current packages used in the course. Topics to be covered on the first day include: high-level introduction to facilities for differential expression, gene sets, genetics of gene expression, measurement of CNV; sketch of the R 2.7 language and analysis environment; Bioconductor containers and annotation facilities. The second day will be devoted to case studies in differential expression, genetics of gene expression, analysis of CNV.

Rockfeller leads: Creative Commons License Goes Mainstream for Science

As noted in this announcement from Science Commons:

"The [Rockfeller] Press adopted a new copyright policy that returns essential freedoms to authors and extends permissions to the public that are vital to advancing science. This new policy covers its journals, which include the prestigious Journal of Cell Biology, The Journal of Experimental Medicine and The Journal of General Physiology."

See the original announcement for details