What is the evidence?

This recent announcement of the lack of efficacy of a widely prescribed "cholesterol lowering" combination (two drugs) agent should give us pause. Those of us who practice medicine know all too well how much of what we do is art and not science. Despite billions of dollars of research that linked blood biomarkers such as LDL and CRP to heart disease, we now have a well-run trial that seems to show that the lowering of these "bad" biomarkers does not affect thickening of the walls of arteries in a manner previously thought to result in disease. This once again points to the importance of unimpeachable curation of medical evidence and its clear and untrammeled communication to patients and providers alike.

No sound before its time?

This late breaking story about the recovery of the sound of a French recording, predating Edison's famous recording has relevance to our modern efforts in digital document archiving. Apparently, Edouard-Leon Scott was able to record sound but not in a way that his contemporaries could play back. It makes the point that archives that do not provide for an immediate "read out" can easily be lost to posterity even if they are physically durably accessible. This is the distinction between light and dark archives.

Notable Book: Inhuman Research, 5.13.08

Every year, we showcase 3-5 notable books. This one, written by Alfred Pasternak, I discovered through the outreach efforts of the Wiesenthal Museum for Tolerance in LA. Dr. Pasternak will be joining us on May 13th for a presentation at 4pm, followed by book signing. He will be accompanied by Ms. Liebe Geft, the director of the Museum of Tolerance, so I am quite sure it should make for a very interesting couple of hours.

Large-scale extraction of gene-level physiology from the bibliome

If you have performed an expression microarray experiment, or a genome-wide association study, or a high-throughput proteomic experiment, you will have had a librarian moment. In that moment, you wish that someone would have organized all that had ever been written about the genes or segments of the genome that came up in your experiment as "significant," typically by some statistical measure. The alternative of having to read hundreds if not thousands of papers is unappealing. Because that librarian moment is so common in this genomic era, a slew of companies have emerged to provide a systematic annotation linked to the literature. In these endeavors, Their ambitions greatly surpass those of the ontologists who are "merely" satisfied with a a few labels for each gene regarding biological processes, functions and cellular locations and they seek to provide whole pathways of gene regulation, and signaling. For this reason, I was quite intrigued by a presentation I recently heard at the C-SHALS conference in Cambridge, MA by a bioinformatics group at Sanofi Aventis. They provided that all too rare and extremely valuable style of review in biomedical science: The consumer report format. That is, they compared several of the leading bibliome-based gene annotation packages and systematically reviewed coverage and specificity of these competing wares. These products fell into two categories: those generated by human curation (Ingenuity, and GeneGO) and those by automated means (Temis, Ariadne). From my perspective the bottom-line was a) the coverage of all these packages is spotty and remarkably non-overlapping (of genes and processes) and b) the human-driven packages were dramatically better in several dimensions. Another full-time Librarian Employment Act, if librarians take this challenge of annotation as their own.

Technorati Tags: Informatics, Scholarship

Absence of a plan

Oya Rieger has produced a very useful and mercifully brief report for the Council on Library and Information Resources. She quickly brings us up to speed on the various large-scale digitization initiatives, reviews who the key players are and reveals, alas, that libraries are followers not leaders in these initiatives. Moreover, she also highlights the lack of a national plan for digital preservation and the myopic lack of coordination across libraries. Particularly revealing was the evidence of the sweeping aside of the meticulous but laborious curatorial plans concocted by librarians. In order to achieve the efficiencies required by the commercial partners who, of necessity, wished to measure success in years and not decades or centuries, These prior plans were greatly simplified and curatorial judgement replaced by broad and blunt heuristics. The report ends with a number of useful suggestions, many of which will require significant changes in the sociology of library stewardship.

Technorati Tags: archives, Collections, Open Access

HMS Rewind: Harvard Medical School 1997

For those of us born before 1990, it may be hard to remember just how recent a development the web is. The Wayback Machine however provides a remarkable glimpse into how far we have come. Contrast this 1997 Harvard Medical School site with this one. Of course, if you are entering the class of 2011, the World Wide Web has always been an online tool. For these students, the preservation of digital content is taken for granted but with exceptions such as the Internet Archive (which depends on philanthropy and grants) huge tracts of this content are dissolving irretrievably.

Technorati Tags: archives, Collections, History, Scholarship

Do we have enough informaticians?

It is generally agreed that we do not have enough informaticians. National organizations have posited that we need to have at least 10,000 informaticians by 2010. Other countries are investing heavily in such training. In Germany, for example, the number of graduates with degrees in informatics has doubled since 1997. But what are these informaticians supposed to know? Answering this question would go a long way to determining just who should be trained and for what purpose? Should they be able to answer these questions? Or should they be able to answer these? Further, should it be MDs that define the competence requirements or could it be nurses, or librarians? More to the point, why don't informaticians collaborate and share their expertise with individuals of other disciplines? And vice versa. For that matter, can informaticians of different stripes identify a common set of skills or is informatics going to balkanize into isolated sub-discplines? These questions point to the increased centrality of information sciences to the pursuit of clinical care and biomedical research and the resulting push to speciation to meet the varied needs of these biomedical constituencies.

Technorati Tags: academics, Informatics

Reference your open access articles for your NIH grants starting April 11th.

As per this NIH policy, all grants submitted after April 7th, 2008 should reference your open access articles. If you are faculty at HMS, the Countway Library will provide support for you to ensure that all the publications heretofore that result from NIH funded research will be available as open access articles.

Technorati Tags: academics, Open Access