NPR has a story today on Morning Edition about the increasing intrerest in the Do Not Track option that online services are supposed to be offering to their customers. I didn’t hear all of it, but I heard enough to draw the conclusion that the usual Washington tug of war is in full swing as threatened interest groups try to de-fang a proposal that might benefit the ordinary Joe or Jane and cost the Interests some money in so doing. OK, there it is: a Bolshie statement about the need for government control of predatory capitalist actions. At issue seems to be the concept of “privacy”. Well, what do you mean by that anyway? Blah,blah. Yak, yak. Lobby, lobby, Sell-out, sell-out. What I mean, Congress persons and regulators, is this: when I click the Do Not Track button I expect the online site, to, well, let’s see, how can I put this: I expect it, indeed I urgently require it, not to track. Anything. At all. Anytime. Ever. I accept the possibility that I might miss out on Great buys in power tools this month, or newly released jazz albums I might like. But, I prefer, like Scrooge, to be left alone. DO NOT TRACK. I hope this contribution to the discussion helps a little bit. Thank you and good day.
There is a new version of the National Library of Medicine’s web site. Some features and services have been re-arranged. There is a new color scheme, etc. But most of your old favorites are there. And it seems to me that there is more glitz and pow! than before. That’s an impression.
Modern health care providers have to deal with a multitude of drugs, and there are a number of sources which can be consulted for information on them. But one of the slickest and most easily consutled is the Drug Information Portal at the National Library of Medicine. We are supposed to be covering this side of things for our readers, but, frankly, haven’t been doing as much of this as we would have liked, or should have. So, in an effort to catch up a little, here is a down payment: get used to thinking about Drug Information Portal when you have a drug question. And before I get too far along in this report, let me give you the link:
DIP has a simple search interface, but if you poke a little bit you will see that there are some interesting features you can use, if you want to. “Truncation to the right”, as we call it in the trade, will let you retireve products with a common stem. Brom*, for instance, retrieve both bromide and bromine in one step. There is also a nifty “truncation to the left”, which lets you stem on an embredded root and pick up alternative prefixes. Putting a truncation character at each end of a search string can bring up compounds. Not many search systems have these last two features, at least not among their documented operators. OK, enough searcher geekery. DIP also allows browsing by category: anti-anxiery agents for example. There is a “pill finder” utility, linking to NLM’s Pill-Box program, outlinks to more searching systems, summaries of product information, dosage guideline and a great deal beyond what I can tell you in a short post. So, write this in your notebook for 2011: Resolution: use Drug Information Portal.
Starting soon, there will be a change in the way PubMed displays abstract formats. Read about the Structured Abstract at this link:
It’s pretty lame, I have to admit, but it’s Monday and I’m just coming back from a bad shaking up I got from a bike accident. I don’t think this blog has been doing enough to cover the widening scandal of ghosted articles in the medical literature. We talk about it among ourselves, the librarians I mean, and there is an active discussion among some faculty here, but over all, I feel I’ve let the side down somehow. So, it’s time to redress the balance, and we’ll start by bringing to our readers’ attention a story that ran in the New York Times of Friday last, in the Business section. The paper is running a series of articles on the topic of ghostwritten articles in medical journals. Ghosted articles are those written at the behest of a drug company, by a firm of “medical educators”, and then circulated to some “key opinion leaders” in the field, with the suggestion that they review and submit these articles for publication under their names, and receive a suitable expression of corporate gratitude for their cooperation. Nobody knows for sure how many such articles are in the medical literature, serving as the basis for research efforts and patient care decisions. But, the orotund Latin phrase non pauci, not a few, comes to mind. Well, there are some “issues” here, as they say, and I don’t want to review the whole topic in this post. I do want to highlight one reaction to the whole mess by one editor of a major journal, Dr. Cynthia E. Dunbar, editor in chief of BLOOD. In brief, her response is “get rid of them”, and perhaps bar the submitting author from furter publication in the journal, at least for a period of years. Needless to say, such action would also lead to considerable bad odor in whatever professional community we happening to be discussing, so it’s a pretty big stick. Journal editors have been accused of being too wussy on the question of “undisclosed contributions”, let’s call them. So the BLOOD action ups the ante quite a bit. PLoS Medicine has also suggested a stance of zero tolerance on ghosting. And Sen. Grassley of Iowa has been after journals to see what kind of policies they have on the matter and is not really satisfied with the replies. My own idea is to ask the National Library of Medicine to introduce a new publication type, Advertisement, and then request that this be applied to any discovered ghosted article. The withdrawal problem would take care of itself, as authors begged to have their offending articles withdrawn. Who, after all, wants to be unveiled as a corporate shill?
The Times piece has several internal links which are worth following:
The National Library of Medicine uses a thesaurus of standard terms to describe the subject contents of the materials it indexes. Medical Subject Headaings, or MeSH, is updated every year and is the only nomenclature which gets this treatment. The other big scientific indexing services, such as Chemical Abstracts, update, for sure, but not annually. MeSH 2009 is in place and is now being used to index articles for MEDLINE and other services offered by NLM. You can read about the new terms in a summary article here:
Terrible, terrible I admit, but how often do you get a chance with something like this. It’s like walking into a room and finding the pen of your aunt on the table. I defy you NOT to say: “la plume de ma tante…” JoVE is the Journal of Visualized Experiments. And, the National Library of Medicine has decided to index these visual productions for inclusion in PubMed/MEDLINE and then to be archived in PubMed Central. MEDLINE used to be restricted to journal literature, pretty strictly, despite a few experiments along the way. But it’s clear to everybody that dissemination of scientific information is not, and can’t be, confined to printed sources, and that the discovery systems which were in place to monitor publication in the various subject areas will have to change some of their rules for inclusion. Items from the Cochrane Library and from the Current Protocols series are already indexed for MEDLINE, but this is the first time a non-printed resources has been introduced into the database. JoVE looks like an interesting critter. Here’s the link to the JoVE official blog and you can review progress so far.
If you haven’t looked at PubMed for a while, you should. The first screen you see after connecting to the service has a football-field size notice about the obligation of all authors funded by NIH to deposit with PubMed Central a copy of the the final approved manuscript describing any research supported by such grants. OK,so it’s not quite as big as a football field, but it takes up a good chunk of screen. There are also links to the lists of journals which take care of this deposit responsibility without the author’s having to do it, and to the site at which investigators can upload the work to PMC.
While we are on the topic of PubMed, we should inform our readers that the Elves in the back room have been tinkering with what is described as an Advanced Search Mode for literature searching. A beta version is available for testing, and those of you who want to try it can do so by entering a search on the PubMed query line and clicking the GO button. On the next screen you will see, very discreetly poised to the right of the query line, a blue link to the current instantiation of the advanced search option. So far, it seems pretty much like the “advanced” feature on other web information searching tools….with menus of clickable elements to structure the query in this or that fashion. Old Birds such as the Blogging Grouch remember the days of command line searching, but I won’t bore you with how much better things were way back then…..although they were, by Cracky!
Here’s a quick update on some things that have been happening in Library Land.
The National Library of Medicine’s subject thesaurus, Medical Subject Headings (MeSH), is revised annually and the revision for 2007 has been added to the system. So, searches conducted in MEDLINE through any of the various product interfaces for it (PubMed, OVID, etc) will be using the new indexing and searching vocabulary. Find out more about MeSH:
NLM has been working on the support material for PubMed and has created several interactive tutorials that are task-specific. They cover topics such as searching by author or by journal name, creating saved searches, using MeSH term to create a search. The general PubMed tutorial can be found on the blue sidebar of the PubMed screen. Anybody who searches PubMed should view the tutorial, and re-view it several times a year. Also in the blue sidebar are the HELP and FAQ functions. The HELP contains the various task specific tutorials I just mentioned, and they are denoted by the title QUICK TOUR, next to an image of a snippet of film.
Take a look.
In 2007, NLM will add a resource called Citing Medicine: the NLM Style Guide for Authors, Editors, and Publishers. Unfortunately, I can’t be more precise about the date, but when the product is ready, I’ll post a announcement.
PubMed has established itself as a major searching service for health science investigators and clinicians, since its version of the MEDLINE database is available on the web at any time of day or night, at no charge. The National Center for Biotechnology Information (NCBI) has steadily improved the system over the years, but recently the pace of innovation has quickened. Major changes have been introduced, especially in the manner in which searchers can set limit elements, such as language, age group of subjects, and year of publication. A new display format called “Abstract plus”shows the searcher the narrative abstract of the original articles plus abbreviated citations to the first five references in the Related Articles array which accompanies each PubMed record. NCBI’s managers are determined to help the PubMed searcher derive as much information from searching sessions as possible, in order to help biological discovery. The new features in PubMed are discussed in the New and Noteworthy section of the service’s web page.
New at PubMed