PubMed® Redesign [2] News, webcast

Since last week you can try the redesigned PubMed (see post). There is a link on the PubMed homepage which will connect to a preview version. The direct link to the preview is: http://preview.ncbi.nlm.nih.gov/pubmed.

Notably, the preview version is expected to run for at least two weeks after which the old PubMed will dissapear! (see NLM technical Bulletin, Sept 11) and Twitter). Since the playing time might be very short: start trying the new interface now!

Tried it? Did you fill in the poll: What do you think of the PubMed Redesign?

As announced in the NLM Technical Bulletin (Oct 1) and on Twitter, there will be webcasts Tuesday, Oct 6: 9:00* - 9:30 am, 11:00 – 11:30 am and Wednesday, Oct 7: 1:00  – 1:30 pm, 2:00 pm – 2:30 pm Eastern Time.
(*see here for the corresponding time  in your timezone).

You are advised to read the article, PubMed® Redesign, before you attend the webcast. Only the first 300 participants will be able to attend. However, the Webcasts will later appear at: http://www.nlm.nih.gov/bsd/disted/clinics/pmredesign09.html.

Want to keep uptodate?
Take an email alert or a RSS-feed to NLM technical Bulletin and/or follow @nnlmscr and  @ncbi_pubmed on Twitter.
Twitter Librarians  who may bring you news on the subject: @pfanderson, @shamsha, @alisha764, @uconnhealthlib, @mfenner and sometimes @laikas

PubMed® Redesign is here… to try.

We have been waiting months for it, it has been announced several times, we have seen previews, webinars, small changes were introduced over time, till suddenly, today (30-09-09) there was a bright button on the front page of PubMed inviting you to “Try the redesigned PubMed”.

You can click on the button or go directly to http://preview.ncbi.nlm.nih.gov/pubmed.

As a matter of fact @pfanderson already informed fellow tweeting librarians about the PubMed preview link the day before (see Tweet) and within minutes the entire Twitter Librarian community was buzzing about it (see the start of the discussion, taken from Eagledawg post on this subject). People thought that the link was not meant to be public, because it was picked up from a webinar, and no official announcement had been made. But today the new PubMed (first time I see the ®?) is live -although still optional-, accompanied by an official announcement of the redesign at NLM Technichal Bulletin (later followed by a post on Linkout in the PubMed Redesign).

Patricia has depicted the changes in a Powerpoint Slide (see post at Emerging Technologies Librarian: What I most want to be able to find in the new Pubmed.

My take on this:

• While the front page looks “Functional, clear, ‘modern’” as  someone on Patricia’s blogpost said, I agree with David Rothman, that there are “TONS of wasted screen real estate on that front page”. Why is the search bar hidden at the top?
• The buttons themselves are relatively easy to find and understand. Although some options like “PubMed Quickstart” are not always straightforward (mistaken for “easy search option” instead of HELP). But that is probably just a matter of getting used to the new design.
• But what happens if you search: The Details-tab is no longer there and the History is gone. Yes, Limits, Preview/Index, History and Details tabs’ features have been consolidated in Advanced search (see techbull).
• This means in practice that the front page only lends itself for performing one-search-at-the–time, without being able to check the Details-tab (only indirectly by going to Advanced Search). It needs little imagination to foresee what will happen. Users will type in (“Google”) terms, the combinations of which are inspired by the “Auto suggest” function. There is no way to check the mapping of the words, there is no way to combine MeSH and textwords (unless you know them by head). Basically this search page only lends itself to “quick and dirty searches”, the “One string only”-Google searches. The new PubMed Interface is all about “Serependity”. Some people may like that. I don’t (mostly…).
• Once done it is easier to save the search or take and RSS-feed (but given the quality of the search…) .
• No functionalities have gone, all there has been done is replacing the functions. But this can (and in my view) has implications for the functionality of PubMed itself,
• Thus advanced searchers have to use the “Advanced Search”. But in contrast to the front page this one is full of limits, indexes and bars that should be wisely (and often not) applied. For people searching for evidence this site is not handy at all. In fact, I find it a real nuisance to use.
  I agree with Creaky: some 3rd party tools seem more adequate for beginners/simple searches. But for advanced searches I will move to OVID MEDLINE, for good. Alas I still have to teach my clients and students PubMed. It will be quite a task to see how that can be best done.

So I conclude:

“It is possible that I am about to preach to the choir, but I am going to come right out and say it anyway. I hate PubMed. I hate it with a burning passion. For a site that is as vital to scientific progress as PubMed is, their search engine is shamefully bad. It’s embarrassingly, frustratingly, painfully bad.”

Looks familiar? Anna Kushnir said that almost one and a half year ago... And Anna did get her way. Her ranting elicited a response of Dr. Lipman of the NCBI who reassured her “that a number of changes are underway that will make PubMed work better for her and many other users”. Pubmed is now “easy to use” for people like her. Will there come a PubMed that suits me too?

You may also want to read:

Kraftylibrarian: The PubMed redesign is here

Pubmed changes at the front door (2009/04/01/)

Advanced Neuritis in Pubmed (2009/03/08/)

Pubmed: past present and future – part iii: the future (2008/06/27/)

Pubmed: past present and future – part-ii/ the present (2008/06/15/)

Pubmed: past present and future – part-i/ the past(2008/06/11/)

Using PubMed

• PubMed Quick Start

UpToDate or Dynamed?

Guest author: Shamsha Damani (@shamsha) ;
Submission for the July Medlib’s Round

Doctors and other healthcare providers are busy folks. They often don’t have time to go through all the primary literature, find the best evidence, critique it and apply it to their patients in real-time. This is where point-of-care resources shine and make life a bit easier. There are several such tools out there, but the two that I use on a regular basis are UpToDate and DynaMed. There are others like InfoPoems, ACP’s PIER, MD Consult and BMJ’s Point of Care. I often get asked which ones are the best to use and why. The librarian answer to this question: depends on what you are looking for! Not a fair answer I admit, so I wanted to highlight some pros and cons of UpToDate and DynaMed to help you better determine what route to take the next time you find yourself in need of a quick answer to a clinical question.

UpToDate

Pros:

• Comprehensive coverage
• Easy-to-read writing style
• The introduction of grading the evidence is certainly very welcome!

Cons:

• Expensive
• Conflict of interest policy a bit perplexing
• Search feature could use a makeover
• Remote access at a high premium
• Not accessible via smart phones
• They didn’t come to MLA’09 this year and medical librarians felt snubbed (ok, that is not a con, just an observation!)

DynaMed

Pros:

• Bulleted format is easy to read
• Remote access part of subscription
• No conflict of interest with authors
• A lot of the evidence is graded
• Accessible on PDAs (iPhones and Blackberries included!)

Cons:

• The user interface is a bit 1990s and could use a makeover
• The coverage is not as extensive yet, though they keep adding more topics

A lot has been written about UpToDate and DynaMed, both in PubMed as well as on various blogs. Jacqueline also did a fabulous post of the evidence-based-ness of UpToDate not too long ago. I used to think that I should pick one and stick to it, but have recently found myself re-thinking this attitude. I think that we need to keep in mind that these are point-of-care tools and should not be utilized as one’s only source of information. Use the tool to get an idea about current evidence and combine it with your own clinical judgment when needed at point-of-care. If suspicious, look up the primary literature the good old way by using MEDLINE or other such databases. A point-of-care database will get you started; however, it is not meant to be a one-stop-shop.

I can almost hear people saying: so which one do you prefer anyways? That’s like asking me if I prefer Coke or Pepsi. My honest answer: both! (databases as well as beverages!). So what is a busy clinician to do? If you have access to both (or more), spend some time playing with them and see which one you like. Everyone has a different searching and learning style and it is sometimes a matter of preference. DynaMed’s concise structure may be appealing to newbies, whereas seasoned clinicians may prefer UpToDate’s narrative approach. Based on my very unscientific observation of Twitter conversations, it appears that clinicians in general prefer UpToDate whereas librarians prefer DynaMed. Could this be because UpToDate markets heavily to clinicians and snubs librarians? Or could it be the price? Or could it be the age-old debate on what is evidence? I don’t know the answer, partly because I find it all a bit too political. I’ve seen healthcare providers often use Google or Wikipedia for medical answers, which is quite sad. If you are using either UpToDate or DynaMed (or another similar product), you have already graduated to the big leagues and are a true EBM player! So relax and don’t feel like you have to pick a side. I find myself using both on a regular basis; the degree of success I have with each can be gauged by my daily Twitter feed!

Shamsha Damani

10 + 1 PubMed Tips for Residents (and their Instructors)

The next Grand Round, the weekly rotating carnival featuring the best medical blog posts, will be hosted by Edwin Leap, a practicing emergency physician. Because the  Grand Rounds are on June 30 -one day before July 1st, which is the traditional start of that thrilling and harrowing journey called ‘residency,’- Edwin decided to make the following theme: ‘What would you like to say to future physicians?’

I’m sure doctors will give plenty advice on the skills that are most important (i.e., see here). But what advice can I give them? I’m not a doctor. I could give them some examples of “how not to behave”, but I’m sure that will be covered well by fellow patients, and probably also by blogging nurses (i.e. see the perfect Intern Survival Guide by Mother Jones RN).

So I will stay with my expertise: searching. And to make it workable, I will restrict myself to PubMed, the platform that offers free  access to 18 million citations from MEDLINE and other life science journals. 18 million, that is a tremendous amount of literature! And that is one of the main problems: the sheer amount makes it very difficult to “pick the needle from the haystack”.

Of course, literature searching is not a primary skill for doctors. It is far more important that a doctor is knowledgeable, handy, and a good communicator (!). But at one time or another, he/she has to look things up or wants to check whether current practice is the best way. Or at the very least, doctors have to stay on top of the best and  latest information. And that’s when they need to search for medical information.

Below are some tips for beginning as well as more advanced PubMed searchers. Obviously, these are only tips, this post is no tutorial and I give but a few elaborate examples. However, I plan to show entire searches in future posts. Perhaps you can help me by sending in examples or asking questions/propose cases.

Here are the 10 PubMed tips:

Tip 1 : Look before you leap.
Before even thinking of going to the PubMed site, consider whether this is the most obvious source to begin with. First decide whether you have a back- or a foreground question.
A background question asks for general knowledge and/or “facts” (questions often starting with who, what, when, why, which). “How can one  diagnose appendicitis?” “Which treatments are available for advanced prostate cancer?”  These questions can be best answered by textbooks, handbooks and certain databases. UpToDate is usually perfect for these kind of questions. A question like “Which dose of drug X should I prescribe to a woman of 65 kg with disease Y.” looks very specific, but can generally be looked up in a Pharmacopeia (“general knowledge”). Some subjects are covered by in-house protocols or specialist guidelines.

When you have a foreground question it is often better (especially for those “new” to the subject) to search evidence in aggregate or pre-filtered resources, like National Guideline Clearinghouse, the TRIP-database and/or the Cochrane Library. This will save you time, because it lowers the number needed to read: individual studies have been sought, selected, appraised and summarized for you.

Besides PubMed there are also so called 3rd party Pubmed/MEDLINE tools, which can be handy for certain questions or approaches. I’m in the middle of writing about these tools, so keep in touch. Meanwhile you may want to read an excellent overview of many of these tools and more on the blog of Mike Cadogan: Medical search for physicians. Earlier I also wrote about the handy use of PubReminer and GoPubMed to analyze text words and MeSH-terms.

Although very useful and intuitive, most of these 3rd party PubMed tools don’t have the power of PubMed and are not suitable for elaborate searches.

Tip 2: A review article from PubMed.
PubMed can be useful for quickly finding good reviews.
Below is one such example. A few months ago, Bertalan Mesko (intern then) asked advice on twitter, because his professor had difficulties finding the cause of recurrent acute pancreatitis in a young adult. Considering this was a background question- I just did a quick and dirty search as follows:

• Go to PubMed: www.pubmed.gov
• Type acute pancreatitis in the search bar (pancreatitis may be ’safer’, but will yield more results).
• Click the Limits Tab and tick off the following options:
  • Facultative: Links to free full text (if you have no subscriptions/access to the medical library)
  • Facultative: Added to PubMed in the last 5 years (or read the first few hits)
  • Subsets: Core Clinical Journals
  • Type of article: Review
  • Tag-Terms: Title.
• Click: Go
  
  

So you search for acute pancreatitis in the title of review articles in core (English) clinical Journals. There are just 28 results in the last 5 years, including reviews in the Lancet and NEJM.

The Lancet review gives me a good suggestion:

In most patients, acute pancreatitis is caused by gallstone obstruction or alcohol, and no genetic testing is needed. However, unexplained recurrent acute pancreatitis might be associated with known genetic mutations in the cationic trypsinogen gene protease serine 1 (PRSS1), SPINK1, or CFTR. Mutations in the PRSS1 gene are seen in most patients with hereditary pancreatitis. In the most frequent mutations, the function of trypsinogen is increased, causing premature enzyme activation and autolysis of acinar cells.

Note that I didn’t limit on age and I didn’t add recurrent to the search, as I’m looking for a review that may discuss many forms of this disease in all age categories. Recurrent or young adult may not be mentioned in the abstract (nor in the MeSH), so I may miss important overviews if I add these terms to my search.

If you get to many hits,  you may always narrow the search later.

A similar approach has been used by drW to search for review articles on heparin induced thrombocytopenia (part 1 and 2).

UpToDate is a good source as well, ..and clinical experience. Ves Dimov responded on Twitter that he had described a similar hereditary pancreatitis case on his blog.

Note that at the end of the summer Limits will be under the Advanced Search.#

Tip 3: PubMed is just one NCBI-database.
As you may infer from the official web address of PubMed: http://www.ncbi.nlm.nih.gov/, PubMed is (just) one of the (freely available) databases of NCBI (National Center for Biotechnology Information) . If you click on the NCBI-logo (in PubMed) you reach the Entrez cross-database search page. Most databases are particularly suited for genetics, genomics and proteomics. Several of the residents I know are also involved in research  and may make ample use of GEO (gene expression database) and/or other databases.

If you type for instance acute pancreatitis in the search bar, you see the hits per database, including the PubMed and MeSH database. In this case OMIM seems the most interesting of the genetic databases. OMIM is the “Online Mendelian Inheritance in Man” database. It contains full-text, referenced overviews with information on all known Mendelian disorders and over 12,000 genes and is intended for intended for use primarily by physicians and researchers.

There are 33 hits in OMIM which we could limit further (using the Limit Tab) to for instance the chromosome. Hits 3-5 describes the genes mentioned in the Lancet review and gives references to relevant studies. There is even an overview of labs performing certain tests (see for instance here)

In stead of going to Entrez, you can also directly search OMIM from the PubMed database (see Figure)

Tip 4: Looking up Citations
One of the recent alterations to PubMed is that you can just type the title in PubMed’s search bar to find a specific article. You can also type in other specifications or an entire reference. But it doesn’t always work. When you type Lancet acute pancreatitis you get too many papers (if you would look for a primary study) but if you copy the following reference from Google: Frossard JL, et al. Acute pancreatitis Lancet 2008; 371(9607) you will get zero results. This is because different Journals have different reference-styles (order, initials, punctuation) and people often make mistakes while citing.

Another possibility, much loved by librarians because of its versatility, is the Single Citation Matcher in the blue side bar. # You can fill in any field you like and some fields like “author name” have an auto-fill function.

In this case I searched for the “Author name” Frossard JL (tick “only first author“) and the First page: 143.

I get exactly 1 paper: the correct one.

Tip 5: Saving your search and making alerts: RSS and MyNCBI
It is important for a doctor to keep up with the new developments in your field. There are ample possibilities in PubMed. One is RSS. A previous post descibes how it can be created in PubMed.

Another possibility is MyNCBI. Old fashioned? Not at all. In PubMed, I find it more useful and easier than RSS. You can find MyNCBI at the upper right or in the blue side bar#.

You have to create a free account. Once you do that, you can save searches (single searches or set numbers, but NOT the entire Search History). You can immediately save a search after performing it [1] or you can left-click the set number in the History, in this case #14, and a pop-up with options appears [2]

Searches can be saved, and executed/adapted at later timepoints or can be used to create an alert. Alerts can be mailed at any frequency you like. If searches overlap it is good to combine them, so you don’t read the same items twice (or more).

Other possibilities are: “Save Collections” (individual articles), make filters (see Tip 1) and share them.
The Save function also works in some other NCBI-databases

A nice gadget: under preferences, you can activate a highlight function: When logged in, the terms you search for are highlighted in the desired colors. That’s why acute pancreatitis and review are highlighted yellow in the PubMed search shown above.

For more information see the FAQ

Tip 6: Stop Googling PubMed: why you find too much or too little

O.k. this is something you may not want to give up, because you’re from the Internet generation and you’re used to intuitive interfaces and searching by trial and error. You’re used to just take a glance at the first few hits out of thousands of records ranked by “relevance” , that exactly match the terms you entered.

This is not what you should aim for in PubMed: finding a paper because the authors use exactly the same words as you search for – and looking at the first few hits (there is no ranking in PubMed, hits are shown chronologically) do not necessarily mean it is the most relevant to you.  It only matters if the study answers your question (for your particular patient), and if it is of good quality.

Thus, don’t aim for wording similarities, aim to find the papers that provide you (and your particular patient) with the best answer.

How do you do that?

It depends on your question, but generally speaking it is not the best thing to type a whole sentence or the entire PICO in the search bar.

Usually it is best to search per term and start with the most important term first and leave out the terms that do not really matter.

So how would you search for the following question?

Does  spironolactone (anti-androgenic) effectively reduce hirsutism in a female with PCOS? Is it safe and is it comparable to Cyproterone acetate?

Some people type: PCOS hirsutism spironolactone treatment cyproterone acetate and add gender and age as well. This yields a few results which are on the topic, but yet you may miss the most relevant ones.

A better way is to search for the two most important concepts: hirsutism AND spironolactone and to look for systematic reviews and RCT’s because these provide the best evidence (see TIP 9). If necessary PCOS can be added afterwards.

Treatment is usually a superfluous term. It is (usually) better to look for RCT’s or -second best “cohort studies” (because these are the best study designs assessing effectiveness of interventions). Also take care not to apply unnecessary limits.

Always ask yourself: is this word crucial? And does adding this word/limit reduce the chance that I find a relevant paper?

Tip 7: Use Details to see how PubMed interpreted (mapped) your search

Whether you use tip 6 or not, at the very least, check the translation of your search by clicking the Details Tab. Yes, your search is interpreted or ‘mapped’, didn’t you know? That is usually a good thing, because PubMed’s keywords (MeSH) are automatically found, if you use terms that PubMed considers as synonyms for certain MeSH. This can enhance your search, but sometimes the translation is either wrong or you didn’t use the correct word (according to PubMed).

So if you check the search PCOS hirsutism spironolactone you will see that hirsutism and spironolactone are correctly mapped to a MeSH, whereas PCOS is not. Seeing this you must be alarmed, because it is very likely that there is a MeSH for such a common disease. The correct MeSH is polycystic ovary syndrome. But in this case you might as well leave PCOS from the search.

Sometimes your term is wrongly translated. If you search for (early) mobilization (of patients), PubMed will translate this as: “metabolism”[MeSH Terms] (as well as “metabolism”[subheading], that is a qualification of a MeSH term). You can imagine that this may easily result in many irrelevant papers. Rather you should use MesH terms like early ambulation and/or the opposite: immobilization. (How, I will tell you in advanced Tips, to be published later)

By taking ONE second to check Details you become aware of wrong translations and can do something about it. Exclude the term or modify the search. Or you can see that the translation is ok and leave it like that.

Tip 8: MeSH or textwords?

There are people who merely use MeSH and people who swear by textwords. I use them both.

MeSH are keywords, added by indexers to the record. It would be a pity if you would miss relevant MeSH-terms, because this will inevitably lead to missing relevant articles.

MeSH are incredibly useful for finding a group of diseases. Suppose I would like to search for the usefulness of exercise to lessen fatigue in cancer patients (no matter which cancer). If I just type cancer in the search bar, this term is not only translated into the MeSH neoplasms, but it is also automatically exploded, which means that all narrower terms (terms lower in hierarchy) are also searched for. Thus papers are found whether they are indexed with neoplasms, lymphoma or breast neoplasms.

On the other hand, if you use only MeSH you will miss new non-indexed papers or ‘wrongly’ indexed papers, while some terms may not even have an appropriate MeSH.

Therefore I usually use both MeSH and free textwords.

In the above example it is sufficient to search for hirsutism AND spironolactone. By checking “Details” you know you’re searching for the right MeSH as well.

If the MeSH is very different from the textwords you may search for both , thus: in case of early mobilization you may search:

early ambulation[mh] OR immobilization[mh] OR early mobili* (* means that you truncate the term and find early mobilised/mobilized, moblisation(s) etc. =Note that when you use an asterisk there is no longer any mapping with the MeSH!!).

Tip 9: Searching for Evidence: Clinical Queries or other search filters

When u search for the best evidence, Clinical Queries may be very handy. These are prefab search filters that aim to find the best evidence.

It is best to first search aggregate evidence by using the systematic review filter, which is really much broader because it also searches for reviews of clinical trials, evidence-based medicine and guidelines.

You just can type some terms in the Search box, but I prefer to make a basic search in PubMed’s main page first (to check the terms) and to fill in the set number, i.e. #9, later. (see Figure)

You only get 10 very relevant hits, including one synthesis of evidence in Clinical Evidence, several Cochrane Reviews and other systematic reviews. Since these are all very recent papers you may decide to stop here.
If you like, you can check for individual trials as well by searching by Clinical Study Category (choose the default: therapy narrow and enter search #9 again). This gives 24 hits.

One word of caution: Not all filters are that good. The Systematic Review Filter and the Narrow Therapy filter are quite good for a quick search though. Tip: you can adapt the filters yourselves.

Tip 10: Search Logic (and Boolean operators)

What do you think you search for if you type: hand OR arm AND foot?

You probably mean to search for (hand or arm) AND foot, but Pubmed follows another logic, depending on the order of the words. In this case it puts (invisible) brackets round arm and foot, not hand or arm. Result: you find far more (irrelevant) articles, because you retrieve every(!) article using the word “hand” and a few extra with (arm and foot).

You can keep it under control by placing the brackets yourselves.
With complex searches I rather combine synonyms with OR and  concepts with AND using the history. It looks like this:

(when you don’t add operators PubMed uses the AND-operator, thus #8 #9 means #8 AND #9).
You can add another term to the search as well, or apply a clinical query or limit. The final search you can save in MyNCBI. It shows the search with the appropriate brackets when you execute it.

Besides OR (synonyms) and AND (narrowing) you have the boolean operator NOT.

Please, generally do not use NOT to get rid of articles that are irrelevant, but rather try to select positively. Why? Because by using NOT you might exclude relevant articles.

Suppose you want to find articles about nosebleeds in children by using NOT adults. Then you also exclude articles about adults AND children.

NOT can be very handy however to subtract searches from each other. Suppose you have screened 100 articles (#1) and you get a brilliant idea using another word, which gives set #5. You can go through 120 articles, but you can also subtract the two searches from each other: #5 NOT #1 : and you only have to check 20 instead of 12o records.

Extra Tip (10+1): Use your library and librarian

As an extra tip, this final and probably most useful tip.
Follow library courses if you didn’t do so already during our internship, ask your librarian to help setting up a search for an automatic alert and to deduplicate results from different databases (i.e. MEDLINE and EMBASE) and ask the help of your librarian if you want to perform exhaustive or difficult searches or if you just want some advice. It is no shame to go to your librarian. We’re there for you.

Let me end with a statement of a fellow librarian (Suzanne Bakker, freely adapted):

“Doctors learn what a Hb-test is, but that doesn’t mean that they have to do the lab test themselves, each time a patient needs a test?! The same applies to searching. It is good that doctors learn the basic stuff, and understand some pitfalls, but they need not become information specialist”

You don’t need to become an information specialist to become a very good doctor…

———————————————–

#Some functionalities may move from the current page (tabs and blue side bar) to the advanced search this summer

Note: Thanks to Edwin Leap who had the patience to await my post, while it was going out of hand and getting much bigger than intended…

LOL: NCBI ROFL

The last few days various people on Twitter (first: DoNotGoGently) tweeted about a hilarious website: NCBI ROFL (http://ncbirofl.blogspot.com/).

At first site this looks like a contradiction in terminis: NCBI (National Center for Biotechnology Information – that houses Pubmed) and ROFL (slang for Rolling On the Floor, Laughing). However, NCBI ROFL is exactly what it is: Rolling on the floor laughing about real scientific papers cited in PubMed. Hence the subtitle: “Real Articles, Funny Subjects”.

NCBI ROFL is the brainchild of two Molecular and Cell Biology graduate students. But everyone is invited to send in new ROFLs.

What are the articles everybody is ROFLing about? A few examples:

• Optimizing the sensory characteristics and acceptance of canned cat food: use of a human taste panel.
• Pigeons can discriminate “good” and “bad” paintings by children.
• Mr. Bean. an important research tool: Kinematic analysis of facial behaviour in patients with schizophrenia under emotional stimulation by films with “Mr. Bean”.
• Feet rolled over by cars: radiological and histological consideratons from experiments. This is really weird: “A total of 15 detached feet from deceased persons who had donated their bodies to research were rolled over using a VW Passat station wagon. The feet were enclosed in various types of shoes.”

And what a coincidence. One of the first ROFL’s was the following:

• Mandibular angle augmentation with the use of distraction and homologous lyophilized cartilage in a case of morphing to Michael Jackson surgery. (Michael died June 25th)

Kinematic analysis of facial behaviour in patients with schizophrenia under emotional stimulation by films with “Mr. Bean”.Kinematic analysis of facial behaviour in patients with schizophrenia under emotional stimulation by films with “Mr. Bean”.

#CECEM David Tovey -the Cochrane Library’s First Editor in Chief

This week I was attending another congress, the Continental European Cochrane Entities Meeting (CECEM).

This annual meeting is meant for staff from Cochrane Entities, thus Centre Staff, RGC’s (Review Group Coordinators), TSC’s (Trial Search Coordinators) and other staff members of the Cochrane Collaboration based in Continental Europe.

CECEM 2009 was held in Maastricht, the beautiful old Roman city in the South of the Netherlands. The city where my father was born and where I spend many holidays.

One interesting presentation was by Cochranes’ 1st Editor in chief, David Tovey, previously GP in an urban practice in London for 14 years and  Editorial Director of the BMJ Group’s ‘Knowledge’ division (responsible for BMJ Clinical Evidence and its sister product Best Treatments, see announcement in Medical News Today)

David began with saying that the end user is really the key person and that the impact of the Cochrane Reviews is most important.

“How is it that a Senior health manager in the UK may shrug his shoulders when you ask him if he has ever heard of Cochrane?”

“How do we make sure that our work had impact? Should we make use of user generated content?”

Quality is central, but quality depends on four pillars. Cochrane reviews should be reliable, timely, relevant and accessible.

How quality is perceived is dependent on the end users. There are several kinds of end users, each with his own priorities.

1. doctor: wants comprehensive and up-to-date info, wants to understand and get answers quickly.
2. patient: trustworthiness, up-to-date, wants to be able to make sense of it.
3. scientist: wants to see how the conclusions are derived.
4. policy and guideline-makers.

Reliable: Several articles have shown Cochrane Systematic Reviews to be more reliable then other systematic reviews  (Moher, PLOS BMJ)*

Timely: First it takes time to submit a title of a Cochrane Review and then it takes at least 2 years before a protocol becomes a review. Some reviews take even longer than 2 years. So there is room for improvement.

Patients are also very important as end user. Strikingly, the systematic review about the use of cranberry to prevent recurrent urinary tract infection is the most frequently viewed article,- and this is not because the doctors are most interested in this particular treatment….

Doctors: Doctors often rely on their colleagues for a quick and trustworthy answer. Challenge: “can we make consulting the Cochrane Library as easy as asking a colleague: thus timely and easy?”

Solutions?

• making plain language summaries more understandable
• Summary of Findings
• podcasts of systematic reviews (very successful till now), .e. see an earlier post.
• Web 2.0 innovations

Key challenges:

• ensure and develop consistent quality
• (timely) updating
• putting the customer first: applicability & prioritization
• web delivery
• resources (not every group has the same resources)
• make clear what an update means and how important this update is: are there new studies found? are these likely to change conclusions or not? When was the last amendment to the search?

I found the presentation very interesting. What I also liked is that David stayed with us for two days -also during the social program- and was easy approachable. I support the idea of a user-centric approach very much. However, I had expected the emphasis to be less on the timeliness (of updates for instance), but more on how users (patients, doctors) can get more involved and how we review the subjects that are most urgently needed. Indeed, when I twittered that Tovey suggested that we “make consulting the Cochrane Library as easy as asking a colleague”, Jon Brassey of TRIP answered that a lot has to be done to fulfill this, as the Cochrane only answers 2 out of 350+ questions asked by GPs in the UK, a statement that appeared to be based on his own experience (Jon is founder of the TRIP-database).

But in principle I think that Jon is correct. Right now too few questions (in the field of interventions) are directly answered by Cochrane Systematic Reviews and too little is done to reach and involve the Cochrane Library users.

click to enlarge

During the CECEM other speakers addressed some of these issues in more detail. André Knottnerus, Chair of the Dutch Health Council, discussed “the impact of Cochrane Reviews”, and Rob the Bie of the Rehabilitation & Related Therapies field discussed “Bridging the  gap between evidenced based practice and practice based evidence”, while Dave Brooker launched ideas about how to implement Web 2.0 tools. I hope to summarize these (and other) presentations in a blogpost later on.

*have to look this up

NOTE (2009-11-10).

I had forgotten about this blank “citation” till this post was cited quite in another context (see comment: http://e-patients.net/archives/2009/11/tell-the-fda-the-whole-story-please.html) and someone commented that the asterisk to the “the amazing statement” had still to be looked up,  indirectly arguing that this statement thus was not reliable- and continuing by giving an example of a typically flawed Cochrane Review that hit the headlines 4 years ago, a typical exception to the rule that “Cochrane systematic reviews are more reliable than other systematic reviews”. Of course when it is said that A is more trustworthy than B it is meant on average. I’m a searcher, and on average the Cochrane searchers are excellent, but when I do my best I surely can find some that are not good at all. Without doubt that also pertains to other parts of Cochrane Systematic Reviews.
In addition -and that was the topic of the presentation- there is room for improvement.

Now about the asterisk, which according to Susannah should have been (YIKES!) 100 times bigger. This was a post based on a live presentation and I couldn’t pick up all the references on the slides while making notes. I had hoped that David Tovey would have made his ppt public, so I could have checked the references he gave. But he didn’t and so I forgot about it. Now I’ve looked some references up, and, although they might not be identical to the references that David mentioned, they are in line with what he said:

1. Moher D, Tetzlaff J, Tricco AC, Sampson M, Altman DG, 2007. Epidemiology and Reporting Characteristics of Systematic Reviews. PLoS Med 4(3): e78. doi:10.1371/journal.pmed.0040078 (free full text)
2. The PLoS Medicine Editors 2007 Many Reviews Are Systematic but Some Are More Transparent and Completely Reported than Others. PLoS Med 4(3): e147. doi:10.1371/journal.pmed.0040147 (free full text; editorial coment on [1]
3. Tricco AC, Tetzlaff J, Pham B, Brehaut J, Moher D, 2009. Non-Cochrane vs. Cochrane reviews were twice as likely to have positive conclusion statements: cross-sectional study. J Clin Epidemiol. Apr;62(4):380-386.e1. Epub 2009 Jan 6. [PubMed -citation]
4. Anders W Jørgensen, Jørgen Hilden, Peter C Gøtzsche, 2006. Cochrane reviews compared with industry supported meta-analyses and other meta-analyses of the same drugs: systematic review BMJ  2006;333:782, doi: 10.1136/bmj.38973.444699.0B (free full text)
5. Alejandro R Jadad, Michael Moher, George P Browman, Lynda Booker, Christopher Sigouin, Mario Fuentes, Robert Stevens (2000) Systematic reviews and meta-analyses on treatment of asthma: critical evaluation BMJ 2000;320:537-540, doi: 10.1136/bmj.320.7234.537 (free full text)
   

In previous posts I regularly discussed that (Merck’s Ghostwriters, Haunted Papers and Fake Elsevier Journals and One Third of the Clinical Cancer Studies Report Conflict of Interest) that pharma-sponsored trials rarely produce results that are unfavorable to the companies’ products [e.g. see here for an overview, and many papers of Lisa Bero].

Also pertinent to the abovementioned discussion at E-patient-Net is my earlier post: The Trouble with Wikipedia as a Source for Medical Information. (references still not in the correct order. Yikes!)

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• #Cochrane Colloquium 2009: Better Working Relationship between Cochrane and Guideline Developers (laikaspoetnik.wordpress.com)
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How Evidence Based is UpToDate really?

KevinMD or Kevin Pho is one of the top physician bloggers. He writes many posts per day, often provocatively commenting on breaking medical news or other blogposts.

A few weeks ago Kevin wrote a post on comparative effectiveness research [5] (tweet below), which is “(funded) research to evaluate and compare clinical outcomes, effectiveness, risk, and benefits of two or more medical treatments or services that address a particular medical condition” (definition from DB Medical Rants).

Kevin stated that doctors certainly need an authoritative, unbiased, source to base their decisions on and that that kind of information is already there in the form of UpToDate®. According to Kevin:

For those who don’t know, UpToDate is a peer-reviewed, evidence-based, medical encyclopedia [1] available via DVD or online that’s revised every 3 months. It does not carry advertisements, and is funded entirely via paid subscriptions [3]. I am a big proponent, and like many other doctors, could not practice medicine effectively without it by my side.” [2]

Kevin Pho also refers to a recent study showing that hospitals who used UpToDate scored better on patient safety and complication measures, as well as length of stay, when compared to institutions who did not use the resource.[4]

Kevin’s post actually summarized a post of yet another well known blogger, Val Jones MD (dr Val) of Better Health. In her blog post Dr Val wonders whether we should incentivize hospitals and providers to use UpToDate more regularly. Incentives can range from pay for performance bonuses to malpractice immunity for physicians who adhere to UpToDate’s, evidence-based, unbiased, clinical recommendations. According to Dr. Val, this might be an effective and easy way to target the problem of inconsistent practice styles on a national level, since many physicians know and respect UpToDate.[5]

The tweet of KevinMD elicited many responses on Twitter. To read most of the discussion on twitter follow this link.

Below I shall discuss the points addressed in the blogpost of KevinMD and DrVal. When relevant I will show/discuss the tweets as well.***

[1] Is UpToDate Evidence based?
The main discussion point on twitter was to which extent UpToDate is evidence based. As you can see below (the oldest tweet is at the bottom, the newest at the top) the opinions differ as to the level of UpToDate’s “evidence-basedness”. It varies from the one extreme of UpToDate doing systematic reviews and being entirely evidence based (drval) to ‘a slant of EBM*’ (@kevinmd) and UpToDate being an online book with narrative reviews.

UpToDate used to be entirely an online book with (excellent) narrative reviews written by experts in the field. From 2006 onwards UpToDate began grading recommendations for treatment and screening using a modification of the GRADE system. Nowadays UpToDate calls its database an evidence based, peer reviewed information resource. According UpToDate the evidence is compiled from:

• Hand-searching of over 400 peer-reviewed journals
• Electronic searching of databases including MEDLINE, The Cochrane Database, Clinical Evidence, and ACP Journal Club
• Guidelines that adhere to principles of evidence evaluation
• Published information regarding clinical trials such as reports from the FDA and NIH
• Proceedings of major national meetings
• The clinical experience and observations of our authors, editors, and peer reviewers

Although it is an impressive list of EBM-sources, this does not mean that UpToDate itself is evidence based. A selection of journals to be ‘handsearched’ will undoubtedly lead to positive publication bias (most positive results will reach the major journals). The electronic searches -if done- are not displayed and therefore the quality of any search performed cannot be checked. It is also unclear on which basis articles are in- or excluded. And although UpToDate may summarize evidence from Systematic Reviews, including Cochrane Systematic Reviews it does not perform Systematic Reviews itself. At the most it gives a synthesis of the evidence, which is (still) gathered in a rather nontransparent way. Thus the definition of @kevinmd comes closest: “it gives an evidence based slant”. After all, Evidence-based medicine is a set of procedures, pre-appraised resources and information tools to assist practitioners to apply evidence from research in the care of individual patients” (McKibbon, K.A., see defintions at  the scharr webpage). Merely summarizing and /or referring to evidence is not enough to be evidence based.
It is also not clear what peer reviewed implies, i.e.can articles (chapters) be rejected by peer reviewers?

As a consequence the chapters differ in quality. Regularly I don’t find the available evidence in UpToDate. That is also true for students and docs preparing a Critically Appraised Topic (CAT). In my experience, UpToDate is hardly ever useful for finding recent evidence on a not too common question. @Allergynotes tweeted a specific example on chronic urticaria and H. pylori, where the available evidence could not be found in UpToDate.
In an older post (2007)*** @Allergynotes (Ves Dimov) commented on an interesting post by Dr. RW: “Are you UpToDate dependent?” by citing an old proverb: “beware the man of a single book (homo unius libri), which describes people with limited knowledge. The current version of the Internet has billions of scientific journal pages and the answer to your questions must be somewhere out there.” Ves:

“I don’t think anybody should be dependent on a single source. If one cannot practice medicine without UpToDate, may be one should not practice at all.”

Likewise, an anonymous commenter on Kevin’ posts stated:

“Don’t overlook the fact that there is a lot of good research outside of UpToDate. This is a great source, but if it’s your only source you’re closing off a tremendous amount of the literature. The articles are also written by people, and are subject to the biases of individuals.”

In another comment Dr. Matthew Mintz of the excellent blog with the same name puts forward that many of the authors have substantial ties to the pharmaceutical industry, meaning that UptoDate (although not financed) is not completely unbiased.

[2] Usefulness
@Allergynotes rightly states that usability/perceived usefulness my be more important to physicians (than real usefulness) and that we should look at what make UpToDate so useful rather than just say “it’s not EBM”. In one of his posts Ves Dimov (@allergynotes) refers to a (Dutch) paper showing that answers to questions posed during daily patient care are more likely to be answered by UpToDate than PubMed.** At my hospital some doctors (especially intern med docs) consider UpToDate as their Bible. It is without doubt that UpToDate is a very useful source both for clinicians, patients and even librarians. It is ideal for background questions (How can disease X be treated, what is the differential diagnosis?, what might be the cause of this disease?), to look up things and as a starting point. And it has a broad coverage. However the point here was not whether UpToDate is a useful source for clinicians – but whether it is a sufficiently unbiased evidence based source to incentive docs to follow its recommendations and its recommendations alone. Or as Shamsha says it: “I don’t like putting all my eggs in UpToDate’s basket.

[3] Disadvantages/Alternatives
As highlighted by the twitter discussions (read from down up), the major disadvantages of UpToDate are its high pricing, its ridigity, monopolistic tendencies and strict denial of remote access. I don’t know if you have seen the recent post of David Rothman on a very unpolite, aggressive vendor trying to push a trial. Most of David readers guess the vendor was from UpToDate (2nd: MD consult). Is it reasonable to positively discriminate in favor of UpToDate, while not everyone may be able to afford this costly database or may prefer another source? Incentives will only enhance UpToDate’s monopolistic position.
The most ideal situation would be an open source UTD, as suggested by @nursedan. Allergynotes thinks that this should be possible. A role for Web 2.0 in EBM?

It should be noted that (besides the databases mentioned in the tweets) there are also other freely available evidence based sources, like

• National Guideline Clearinghouse (NGC), a public resource for evidence-based clinical practice guidelines
• National Library of Guidelines, a collection of guidelines for the NHS.  It is based on the guidelines produced by NICE and other national agencies. NICE guidelines of very high quality, based on a systematic review of the evidence and extensive consultation with clinicians and patients and, where relevant, industry. Dr. Matthew Mintz also stresses the usefulness of NICE-guidelines in his comment to Kevin’s post
• TRIP database, that grazes various evidence based resources, including the ones above.

[4] Hospitals using UptoDate score better?
Kevin and Dr Val also refer to a study in International Journal of Medical Informatics showing hospitals that used UptoDate scored better than hospitals that didn’t (even in a dose-response way). This study is shown prominently at the UpToDate’s site.

Now let’s just “score” the Evidence.

First one can wonder how representative this article is. A quick and dirty Google search gives many hits on the very same subject not (directly) linking to UpToDate. For instance, a paper published in the January issue of Ann Intern Med tells us the results from a large-scale study of more than 40 hospitals and 160,000 patients showing that when health information technologies replace paper forms and handwritten notes, both hospitals and patients benefit strongly (fewer complications, lower mortality rates, and lower costs). Etcetera. One would like to know how the evidence in the “UpToDate paper” would relate to other studies or even better one would like to see a head to head comparison of UpToDate with any other (specific) evidence based source.

The Impact Factor of INT J MED INFORM is 1.579. This says nothing about its value, but such a paper wouldn’t likely appear in UpToDate’s handsearch list.

More important 2 of the 4 authors are from UpToDate. This is an important bias.

Furthermore the study is a retrospective and observational study, comparing hospitals with online access to UpToDate with other acute care hospitals. According to the GRADE system this would automatically yield a Grade C: low-quality evidence from observational evidence. Most important, as admitted by the authors, the study could not fully account for additional features at the included hospitals that may also have been associated with better health outcomes. It is easy to imagine, for instance that a hospital being able to subscribe to UpToDate has a medical staff that was already predisposed to delivering higher quality care or might have a greater budget . And although the average, severity-adjusted lenght of stay was significantly shorter in UpToDate® hospitals than in other hospitals with a P value of less than 0.0001, the mean difference was only 0.167 days with a not very impressive 95% confidence interval of 0.081–0.252 days.

[5] Incentives?
Based on the above arguments I don’t think it would be reasonable, effective or fair to incentive those hospitals or doctors that consult (and can afford) UpToDate or to indirectly punish those that don’t (because they don’t have the money or they have a good alternative).

Furthermore such a positive discrimination would not solve the problem of lack of head to head comparison, what was what it was all about. Dr Mintz explains this very clearly in his comment to Kevin.

“… the authors of UptoDate are providing their own summary of already published data, which most is funded by industry. This is similarly true of other so-called unbiased sources.(..)
The problem goes even deeper than the potential bias of industry funded research, which has been consistently shown to be favorable to the sponsor. The fact that most research, and virtually all therapeutic research is funded by the industry allows the industry to dictate what scientific knowledge is available, and by default clinical practice.(…)
There are hundreds of important studies that are never done because the industry only takes a “safe” bet.
We need comparative effectiveness not just to see whether the more expensive treatment is worth the cost, but we also need it to answer scientifically important questions that the industry will unlikely fund.”

*EBM = evidence based medicine

** It should be noted though that an other interface of PubMed is used in this hospital, to allow recording of the queries.The study participants were doctors in internal medicine.

*** I’ve added this sentence because people thought I merely summarized the tweets. In addition I added some new references.

References:

• Kevin MD: (2009/03): Do doctors already have a source of comparative effectiveness research?
• Dr. Val Jones from Better Health (2009.02.25) Attention Health Policy Makers: How To Win Docs And Influence Patients.
• R. centor from DB’s Medical Rant: Comparative Effectiveness research (2009/02/23)
  
• UpToDate.com (with info about the database)
• Bonis PA, Pickens GT, Rind DM, Foster DA Association of a clinical knowledge support system with improved patient safety, reduced complications and
  shorter length of stay among Medicare beneficiaries in acute care hospitals in the United States. Int J Med Inform. 2008 Nov;77(11):745-53. (abstract)
• Tweets about UpToDate by several people (shamsha, kevinmd, drval, allergynotes, digicmb, laikas) note that result is not static, several tweets added since this post.
  
• Amarasingham R, Plantinga L, Diener-West M, Gaskin DJ, Powe NR. Clinical information technologies and inpatient outcomes: a multiple hospital study. Arch Intern Med. 2009 Jan 26; 169(2): 108-14
  
• Clinical Cases and Images – Blog. Study: UpToDate More Likely than PubMed to Answer Patient Care Questions (2008/10/)
• Arjen Hoogendam, Anton FH Stalenhoef, Pieter F de Vries Robbé, A John PM Overbeke, D Answers to Questions Posed During Daily Patient Care Are More Likely to Be Answered by UpToDate Than PubMed. J Med Internet Res 2008;10(4):e29) – doi:10.2196/jmir.1012
• Clinical Cases and Images – Blog. Are You Dependent on UpToDate for Your Clinical Practice? (2007/07)
• Notes from Dr. W. Are you UpToDate dependent? (2007/07)
• David Rothman on Davidrothman.net. Venting about a lousy vendor sales rep (2009/03/24)

You may also want to read:

• Walter Jessen on Highlighthealth. US encourages evidence based medicine in economic stimulus (2009/02/17) (2009
• Guest Post of Shamsha Damani: Evidence based medicine the facebook of medicine. (2009/04/04)
• The web-2.0 EBM medicine split (1) introduction into a short series (2009/01/04/) The above post could have been the 2nd in this series,
  

PubMed Changes at the Front Door

This blog has repeatedly discussed the recent and upcoming changes to PubMed (see links below). I didn’t try to hide that I was not impressed with -nor very fond of- most of the changes. But despite these feelings, shared by many (librarians?), the introduced changes are there to stay, whereas the announced changes are about to be implemented…… SOON, VERY SOON!

The most salient changes are the disappearance of the Single Citation Matcher, the Tabs (Limit, Preview/Index, Clipboard, History, etc.) and the Blue Side Bar. Full text icons are already gone (i.e. the green page icon indicating free full text).

Factually, this means that in a short while you can only use the Advanced Search. It will no longer be optional. Besides the shortcomings of this feature (see previous posts), it will also mean that a complex search (when you need to look up MeSH) will take much longer. As discussed before, using “The Index of Fields in the Advanced Search” is not very suitable for this purpose.

As you may know, multi-word terms words are now split and separately searched in all fields instead of searched as one term in title and abstract (ATM or Automatic Term Mapping)* or as Michelle Kraft of “the Krafty Librarian” describes it: ATM is basically just Googlizing the search process.

To get a complete picture of the upcoming changes, I recommend the excellent post of Michelle Kraft describing all these changes in detail (see here).
Michelle also refers to two valuable information sources:

• MidContinental Region (MCR) recording of one NIH webmeeting: https://webmeeting.nih.gov/p67806081/
• Good video for patrons to show them the changes and how to search PubMed: Melissa Rethlefsen’s tutorial at Mayo Clinic.http://liblog.mayo.edu/2009/03/04/pubmed-advanced-search-an-introduction/

To be honest, I fear the upcoming changes. Personally, I already switched to the OVID interface to search MEDLINE, but I’m afraid of how it will affect the search courses we give and the way the patrons will search PubMed. Given the past experiences (usage of wrong MeSH, too easy use of limits, no use of Clinical Queries), I’m not very confident about it.

——————————–

Note: *the mapping process with MeSH terms remains unchanged.

You may also want to read:

• Advanced Neuritis in Pubmed (2009/03/08/)
• Pubmed: past present and future – part iii: the future (2008/06/27/)
• Pubmed: past present and future – part-ii/ the present (2008/06/15/)
• Pubmed: past present and future – part-i/ the past(2008/06/11/)

Advanced Neuritis in PubMed

Almost a year ago (June 2008) I discussed PubMed’s Advanced Search Beta in a series entitled PubMed: Past, Present and Future. At that time I was not particularly impressed by disliked Advanced Search Beta and I still do.

November last year some of its features have improved: like the addition of a Clear Button, Focused Queries, providing links to the Clinical Queries and Special Queries pages, and the author/journal search has been extended with optional fields so that it looks more like the valuable Single Citation Mapper in the blue side bar of the Basic PubMed page. And there is a link to the MeSH-database (see NLM Technical Bulletin November 2008).
Although these are real improvements, the links to the Queries and to the MeSH database are inconspicuous, at the end of the page below all kind of limits. My major objections to the Advanced Search is that people are more inclined to narrow their search by using as many limits as possible (because these are so prominently present) and that the MeSH cannot be easily looked up and/or are wrongly translated. Previously I gave some examples, where lung cancer[mesh] was searched, whereas the MeSH is lung neoplasms, or where recurrent pregnancy loss[MeSH] returns no result, because the term is habitual abortion (see previous post).

I avoid Advanced Search as long as I can, but the problem is, the library-users don’t. They like to experiment, especially when they consider themselves as advanced searchers.

Last month a Neurologist asked me if I could check his search for a Diagnostic Systematic Review. A search for a Systematic Review should be comprehensive and thus contain both MeSH-terms (Controlled terms of MEDLINE) and free text words (tw).

He was a resident in Neurology for 5 years and knew how to search PubMed.

Below is the first part of his search.

((((((((motor neuropathy[MeSH Terms] OR motor neuron[tw] OR motor neuropathy[tw]) OR multifocal motor neuropathy[tw]) OR demyelinating neuropathy[tw]) OR multifocal demyelinating motor neuropathy[tw]) OR neuropathy[tw]) OR neuropathies[tw]) AND (((((((((((((((((((((((((…..

Grosso modo it looked all right and well structured. The awful number of brackets is often seen when people combine directly in PubMed (although I was already glad there were no brackets around every single word and he didn’t copy the entire translation from the Details-Tab). And some terms were superfluous: you don’t have to search for multiword terms with neuropathy (i.e. motor neuropathy) because these are already found by searching neuropathy.

So we made the search simpler, like this:

(motor neuropathy[MeSH Terms] OR motor neuron[tw] OR neuropathy[tw]) OR neuropathies[tw]) AND (………

Just to be sure I asked him: “Do you mind if we check the MeSH? Motor Neuropathy looks just fine, but you never know.”

To my surprise, typing motor neuropathy in the MeSH search bar yielded 4 suggestions, none of which was motor neuropathy.

The most suitable term appeared Neuritis. When bringing this MeSH-term to PubMed we got exactly the same number of hits as with Motor Neuropathy. Mere coincidence? No, the hits weren’t any different (#1 NOT #4 giving zero results).

Looking Up the Query Translation under the Details Tab confirmed my suspicion: motor neuropathy[mesh] was translated as “neuritis”[MeSH]. This is disturbing. Not only doesn’t there exist any MeSH specific for motor neuropathy, people are put on the wrong track since it looks like motor  neuropathy[mesh] is recognized as such.

Then it came to my mind that I had seen a similar odd “translation” when using PubMed Advanced Search (see above). And I asked him: “Did you by any chance use the Advanced Search”, which he did.

To check this I searched in Advanced Search for the MeSH: motor neuropathy. And, yes indeed, the motor neuropathy[MeSH] was searched so it seemed. (in reality we now know: Neuritis was searched). The difference with searching the MeSH database is that here I know that I search for neuritis (I choose to), whereas the Advanced search misleads me by suggesting I’m searching for motor neuropathy.

Why do I bother? Why don’t I just use motor neuropathy[mesh]. First because I don’t get what I want: I get neuritis[mesh] not neuropathy! Second, and most important, because it is not the most appropriate MeSH-term.

To find more appropriate MeSH I use a trick. I look for MeSH-terms assigned to articles, having motor neuropathy in their title, assuming that motor neuropathy is an important aspect of those papers.

Although you can look up MeSH assigned to each individual citation in PubMed in the citation display format, it takes a lot of time to go through the papers one at a time. Therefore I rather use GoPubMed or even better PubReminer for this purpose, because these give you a frequency list of the MeSH assigned.

Of the 379 hits found in GoPubMed, 219 were categorized as Motor Neuron Disease, 153 as Demyelinating Diseases and 145 as Polyneuropathies. These categories are MeSH term you can use for your search.

Similarly of the 380 references found in PubReminer, many papers were indexed with Motor Neuron Disease, Demyelinating Diseases, Polyneuropathies, peripheral nervous system diseases and motor neuron.

(Below are the number of papers, indexed with the indicated MESH in PubReminer; PubReminer shows the subheading coupled to the MeSH)

• 65 Motor Neuron Disease/diagnosis
• 32 Motor Neurons/physiology
• 26 Demyelinating Diseases/diagnosis
• 16 Peripheral nervous system diseases/diagnosis
• 8 Polyneuropathies

Using this approach we were able to set up a more complete search in PubMed. Remember it was the neurologist’s purpose to to an exhaustive search, for a less exhaustive search we would have only used motor neuropath* and perhaps motor neuron disease[mesh].

How different is it when you use the OVID interface for searching MEDLINE.

When you type Motor Neuropathy, several MeSH are suggested, many of which are useful:

When you click on Motor Neuron Disease, you see the hierarchal context and can choose which terms you would like to add. We choose not to explode Motor Neuron Disease, but only include one narrow term in our search: amyotrophic lateral sclerosis.

Finally the first part of the search in MEDLINE (OVID) looked like this. It is rather broad but the second part of the search (not shown) puts it into context.

1. motor neuron disease/ or amyotrophic lateral sclerosis/
2. exp Motor Neurons/
3. Demyelinating Diseases/
4. neuromuscular diseases/ or peripheral nervous system diseases/ or neuritis/ or polyneuropathies/
5. (neuropathy or neuropathies).tw.
6. motor neuron*.tw.
7. or/1-6

OVID MEDLINE was easier to use, you get what you see (and want) and the search is easier to save and edit. Furthermore the entire MEDLINE search can be easily transformed to a search in EMBASE: just replace MESH by EMBASE keywords.

I’m not happy with the Advanced Search for reasons explained above. I don’t find the altered mapping and citation sensor a success either. I don’t like that they removed the blue side bar in some display formats. And I’m really getting depressed by NLM’s announcement (November 2008):

PubMed Advanced Search will soon no longer be a beta site. It is now the place to go to use features such as field searching and limits. In the near future the tabs for Limits, Preview/Index, History, Clipboard, and Details will be removed from the basic PubMed pages. History, Limits, Index of Fields, and a link to Details are available from the Advanced Search screen. A link for the Clipboard appears to the right of the search box on the PubMed screen when the Clipboard has content.

If I understand it correctly this means that Pubmed Advanced Search is taking over the basic search.

It looks that my original idea was right: PubMed is going for the mass, it is going for the Google-like quick searches by people that don’t know much about MEDLINE and don’t want to learn it. But you have to know some basic principles to get the most out of subject searching. It is such a pity, that PubMed tries to copy its clones, whereas it holds all the trumps. No other 3rd party tools offer the same possibilities that PubMed offers, although they are more suitable for certain purposes (see examples of GoPubMed and PubReMiner above).

At least make two interfaces, one for the beginner (the present Advanced Search) and one for librarians and other people doing subject searches.

But I don’t have the illusion that the people of PubMed/NLM will listen to me and I’m not going to contact them for a 3rd time. PubMed’s route is determined, I guess.

Search Filters. 1. An Introduction

I’ll be writing a lot about search filters in the near future. Before I do, I think it would be useful to give an introduction.

First I want to stress that this series will not deal with Google, Twitter etc. search filters. Although I might write about such filters on another occasion, this series is about filters for biomedical bibliographic databases, such as MEDLINE (PubMed) or EMBASE.

Below is a short Dutch presentation on search filters I gave at a symposium on search filters in 2005.[1] (some slides don’t show well in Slideshare)

What are search filters? [1-5]

Search filters are predefined and pretested search queries designed to retrieve selections of records in specified electronic information sources. Usually they are created by librarians, but they can be run by clinicians and researchers as well.

Why are search filters useful?

It is increasingly difficult, especially for the busy clinician, to find the information he/she wants in a database like PubMed. Filters can help to narrow down the search. In this way you can reduce the number needed to read (i.e. in a quick search) and/or increase the number of relevant papers (i.e. for a systematic review).

Different classes of filters:

• Subject vs Methodological Filters
  • Subject filters are search queries for a topic, i.e. the BestBets paediatric filter (to search broadly for articles on children) or the build-in toxicity filters in ALTBIB. Both are search strategies for PubMed.
  • Methodological Filters, Qualitative Filters or Hedges are search strategies designed to find studies with a certain design or methodology. PubMed has build-in methodological filters, the so called Clinical Queries for domains (therapy, diagnosis, etiology/harm, or prognosis) and for evidence based papers (like systematic reviews and guidelines, see Systematic Review subset in Pubmed).
    
• Sensitive vs Specific Filters
  • Sensitive filters are broad filters, designed to find as much relevant papers as possible, often at the cost of much ‘noise’.
  • Specific filters are designed to find a small set of very relevant papers, with the risk of omission of a considerable number of relevant papers.
• Short vs Long Filters
  Filters may be simple -even consisting of one single term- or may be complex. They can comprise keywords, text words or both.
  
• Database and search-interface dependency
  Filters are usually designed for a specific database and interface. Not every filter that has been developed can be directly translated into another database/platform because of different keywords terms, hierarchy of keywords, structure and commands. For instance in EMBASE Case Control Study (which is not strictly a controlled study) is a Narrower term of Controlled Study, together with Controlled Clinical Trial. In MEDLINE Case-Control Studies‘ is considered an epidemiologic study, whereas Controlled Clinical Trials is a Publication Type. Note that the MESH is in the plural form: ‘Case-Control Studies‘
  The OVID platform allows separate searching of the abstract field (command: .ab.), whereas PubMed has no separate command for this ([tiab], title and abstract). Adjacency searching and non-explosion of subheadings (qualifiers of a MeSH term) is also possible in OVID, but not in PubMed.
  
• Time dependency
  The performance of a filter may change over time because other terms may prevail or database keywords may have been added, removed or changed. In PubMed for instance the MeSH Randomized controlled trial has been changed in the MeSH Randomized controlled trial as a topic.
  
• Subjective vs Objective Filters.[1,2]
  • The 1st generation of filters are subjectively derived, based on the expertise of the searcher.
  • 2nd generation is also subjectively derived, but then tested and validated against a gold standard, i.e. a known set of relevant records, to determine the effectiveness of the filter at retrieving relevant records.
  • 3rd generation involve objective approaches to filter design (e.g. frequency analysis or logistic regression). Search filter is tested on an independent set of known relevant records (gold standard).
    Whether filters are broadly applicable to different clinical areas will depend on the choice of the golden standard (subject, publication year, size) and the presence and composition of an extern valididity standard (a set of records different from the records used to develop the filter, against which the developed filter is tested)

Performance measures (for 2nd and 3rd generation filters), Figure adapted from [9]

Sensitivity: The number of relevant records retrieved by the search filter as a proportion of the total number of records in the gold standard.(A/A+C)
Specificity: The number of records that are not relevant and are not retrieved as a proportion of the total number of records.(D/D+B)
Precision: (or positive predictive value), fraction of returned positives that are true positives. (A/(A+B)

Is there any difference between search filters and limits?

Not really, both are search terms that can be used to narrow the search. In PubMed however limits usually consist of ONE single MeSH-term (MEDLINE Subject Headings, i.e. key words assigned by MEDLINE-indexers), thus these limits will miss recent papers that have not been indexed by MEDLINE. Therefore it is often safer to use a broader filter or no limit at all.

For instance consider the search tinnitus AND behavioral treatment (set #1 in the Fig. below). This yields 175 hits.
Most people, if they want to find the best individual studies limit for RCT, i.e. the subject search is combined (ANDed) with “randomized controlled trial[Publication Type]“. This yields 23 hits (#2).
However if they would have combined ther search with the narrow therapy-filter (#3) they would have found 3 extra hits, two of which being RCT’s, but still in process and not indexed:

1: Weise C et al Biofeedback-based behavioral treatment for chronic tinnitus: results of a randomized controlled trial.J Consult Clin Psychol. 2008 Dec;76(6):1046-57.
2: Kaldo V, et al Internet versus group cognitive-behavioral treatment of distress associated with tinnitus: a randomized controlled trial.
Behav Ther. 2008 Dec;39(4):348-59. Epub 2008 Apr 20.

The narrow therapy filter has found these very recent articles, because it not only searches for randomized controlled trial[Publication Type], but also for randomized AND controlled AND trial in title and abstract.
The broad therapy filter (#4) searches for clinical trials in general and finds many clinical trials that are not RCT’s.
The narrow (#5) and broad (#6) Cochrane RCT-filters are highly sensitive search strategies meant to identify randomized controlled filters for a Cochrane Review (see 10).

Thus for a quick search for relevant papers search #3 (narrow therapy filter) is most optimal.

References

1. Limpens J [ppt] Introductie Zoekfilters 2005 (Dutch)
   
2. Booth A (Scharr) [ppt] Quality Search Filters at http://www.le.ac.uk/li/lgh/library/ABooth.ppt
3. Jenkins M. Evaluation of methodological search filters–a review. Health Info Libr J. 2004 Sep;21(3):148-63.
4. Glanville J, Bayliss S, Booth A et al So many filters, so little time: the development of a search filter appraisal checklist.J Med Libr Assoc. 2008 Oct;96(4):356-61.
5. UBC Health LiBrary wiki: Systematic_review_searching and Filters (ie.hedges)
6. Haynes RB, Wilczynski N, McKibbon, KA et al. Developing optimal search strategies for detecting clinically sound studies in Medline. J Am Med Inform Assoc. 1994 Nov-Dec;1(6):447-58.
7. PubMed Clinical Queries
8. Systematic review subset in PubMed
9. McKibbon, KA, Wilczynski, NL, Haynes, RB Retrieving randomized controlled trials from medline: a comparison of 38 published search filters. Health Info Libr J. 2008.
10. Post: New Cochrane Handbook: Altered Search Policies.

Reference Management Software, Shut Down of 5 Google Apps and a Plane that Crashed.

Reference Management software, shut down of 5 Google apps and a plane that crashed. What have they in common? Nothing, except that these three unrelated subjects all reached me via Twitter last Thursday eve.

[1] When I checked my Tweetdeck (a twitter client) I saw a huge number of tweets (twitter messages) about the crash of a plain in the Hudson river. It now appears that Twitter and Flickr broke the news 15 minutes before the mainstream media. Below is the first crash picture which was posted on Twitter from an iPhone, taken by Janis Krums from a ferry. Earlier (Twitter as a modern tam tam) I gave some other examples of Twitter as a breaking news platform.

[2] Twitter is also a useful tool for up to date information and exchange of thoughts. For instance some tweeple (people on Twitter) had been asking about free reference management software. I had retweeted (RT, resend) the message and Thursday eve DrShock (of Dr Shock MD, PhD) tweeted a very useful link to Wikipedia which compared all reference management software, which was retweeted to the Twitter community.

The wikipedia article gives a comprehensive overview of the following software: 2collab, Aigaion, BibDesk, Biblioscape, BibSonomy, Bibus, Bookends, CiteULike, Connotea, EndNote, JabRef , Papers, ProCite, Pybliographer, refbase, RefDB, Referencer, Reference Manager, RefWorks, Scholar’s Aid, Sente, Wikindx, WizFolio, Zotero.

The following tables are included: the operating system support, export and Import file formats, citation styles, reference list file formats, word processor integration, database connectivity, password “protection” and network versions.

Very useful (although not always accurate). See: http://en.wikipedia.org/wiki/Comparison_of_reference_management_software.

[3] @Symtym (of the blog Symtym) had just learned me how to use Google Notebook to clip and collect information as you surf the web, organize the notes in notebooks and publish the public notes automatically to twitter via twitterfeed. I found it real handy and gathered some material to write a post about it.

But then came the news, brought to me by @Dymphie (of Deetjes (Dutch)), that Google decided to close many services, including Notebook as well as Google Video, Catalog, Jaiku, Dodgeball) or as ReadWriteWeb says it: “Google Giveth, and Taketh Away”. (see announcement on the Google Operating System blog).

Although Google Notebook itself will remain, the active development will be stopped. Of course this was shocking for many faithful users, including me, Dr. Shock and many others (see comments here)

What are the alternatives? Soon @DrCris, author of several blogs including Applequack, tweeted on a solution soon to come: “Evernote is working on a Google notebook importer“. I heard great things about Evernote, many doctors seem to use it, so I might as well give it a try.

Diigo is also planning to make a GN importer (see here). Presumably other tools will follow soon.

Note added:

Two articles in Lifehacker give tips [1] “where to go when google notebook goes down” and [2] describe how you can import the entirety of your google notebook to ubernote (Thanks Dr.Shock.)

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“Reference Management software, shut down of 5 Google apps and a plane that crashed”. Wat heeft dit met elkaar te maken? Niets eigenlijk, behalve dat ik donderdagavond hiervan via twitter op de hoogte gesteld werd.

[1] Eerder gaf ik al voorbeelden dat twitter als een moderne tam tam werkt en vaak een primeur heeft. Donderdag was dat ook het geval. De eerste berichten van het neerstorten van een vliegtuig in de Hudson rivier kwamen via twitter binnen.

[2] Twitter is ook nuttig om informatie te delen. Deze week vroegen mensen naar gratis reference manager software. Ik twitterde dat door (RT of retweet) en donderdag kwam @DrShock (van Dr Shock MD, PhD) met een erg nuttige link naar een artikel in wikipedia. Vervolgens werd door ‘retweeten’ een groot aantal volgers op de hoogte gesteld

In het artikel wordt de volgende software vergeleken: 2collab, Aigaion, BibDesk, Biblioscape, BibSonomy, Bibus, Bookends, CiteULike, Connotea, EndNote, JabRef , Papers, ProCite, Pybliographer, refbase, RefDB, Referencer, Reference Manager, RefWorks, Scholar’s Aid, Sente, Wikindx, WizFolio, Zotero met betrekking tot de volgende punten: “the operating system support, export and Import file formats, citation styles, reference list file formats, word processor integration, database connectivity, password “protection” and network versions”.

Heel erg nuttig en overzichtelijk (in tabelvorm met kleurtjes). Zie: http://en.wikipedia.org/wiki/Comparison_of_reference_management_software.

[3] Van @Symtym (blog: symtym) had ik juist geleerd hoe ik Google Notebook kon gebruiken om teksten al surfende op het net te knippen, bewaren en verzamelen in kladbloks en vervolgens te publiceren op twitter via twitterfeed (berichten automatisch ingekort tot 140 lettertekens). Ik vond het ontzettend handig. Het is een ideale manier om snel informatie te organiseren om later te bekijken, om er een stukje over te schrijven en/of om direct met anderen te delen.

Maar toen kwam als donderslag bij heldere hemel het nieuws via @Dymphie (van Deetjes) tot mij dat uit verschillende Google applicaties de stekker zou worden getrokken. Ook uit Google Notebook. En daarnaast Google Video, Catalog, Jaiku, Dodgeball).

Google Notebook zelf zal nog wel even blijven, maar de ontwikkeling zal worden stopgezet. Natuurlijk is dit nogal een schok voor trouwe gebruikers. Eerst worden mensen geenthousiasmeerd om een nieuwe tool te gebruiken en vervolgens wordt deze hen weer ontnomen

Gelukkig twitterde @DrCris, auteur van o.a. Applequack, vrijwel direct dat Evernote werkt aan een Google notebook importeerfunctie. Ik heb erge goede dingen gehoord van Evernote en veel artsen gebruiken het, dus ik ga dat ook maar eens proberen. Diigo is ook bezig met het ontwikkelen van een GN importeerfunctie (zie hier). Waarschijnlijk zal dit wel navolging krijgen. Toch blijft het vervelend om steeds maar van tool te moeten veranderen. Maar misschien moet je dat op de koop toenemen bij gratis applicaties.

Achteraf toegevoegd

Twee artikelen in ‘Lifehacker’ gaan over dit laatste punt [1] “where to go when google notebook goes down” en [2] describe how you can import the entirety of your google notebook to ubernote (Met dank aan Dr.Shock.)

Temporary Wrong OVID EMBASE Source Field.

This post is only of interest to those who regularly search the EMBASE database from OVIDSP and load the records into Reference Manager or other reference management software, like Procite.

My colleague, Arnold, noticed that off half November the EMBASE records wouldn’t load properly into Reference Manager. This was due to the inclusion of the Publisher in the Source field.

New:
Source European Journal of Surgical Oncology. W.B. Saunders Ltd. 34(12)(pp 1285-1288), 2008. Date of Publication: December 2008.

Old:
Source European Journal of Surgical Oncology. 33(4)(pp 524-527), 2007. Date of Publication: May 2007.

Unfortunately it was not possible to make a new, completely working EMBASE-import filter.

Meanwhile our library has contacted OVID and they have restored the problem quite smoothly. The problem was apparently caused by the EMBASE reload of November 17th.

If you have loaded EMBASE records during the last 3 weeks it might be worthwhile to reload them in your reference manager software. Old EMBASE-filters should do the thing.

Another Search Bug? Now in the Cochrane Library!

It seems that I’m becoming an expert in search problems and bugs.
Partly because I search a lot, but also because my colleagues and I often share our search problems.

This time, while giving a class, Hanny and Heleen noticed that (a) combining two terms in the Cochrane Library Search Bar with ‘and’ gives less hits than when you (b) search for those terms individually and combine them in the History with ‘and’ (see Figures). This is odd, because it should not make any difference whether you look these words up individually (which takes more time) or combine them directly. The field in which both these terms should occur is in the title, abstract and/or keyword field.
(c) Searching via advanced search has the same effect as searching the terms separately in the search bar (#7, #9)

The 3 search modes (click to enlarge)

Two examples are given below: (1) obesity and sibutramine (sets #1-#9) and (2) sibutramine and body weight (#10-#14).
Both obesity and body weight are MeSH (key words from MEDLINE).

Search History showing results two examples (click on Figure to enlarge)

It is unclear why certain records can’t be found when combining them in the search bar. The order doesn’t matter, for instance. It might have something to do with certain keywords not being found when the keyword command is not directly next to term sought (set #12 in Search History, and figure below).

Anyway this is highly undesirable. Especially for the beginner, who just wants to find a cochrane systematic review by doing a quick search. Hopefully this ‘bug’ will be fixed soon, because important papers might be missed (see below).

Missed papers (have one of the terms exclusively in the keyword (MeSH)section

Another bug in My NCBI?

This bug is now fixed (15-11-2008) !!!

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It is confusing, but each week I have another post on the appearance, disappearance or reappearance of a bug in PubMed’s My NCBI:

• October 1: the (History) set numbers could not be saved in PubMed’s My NCBI (Saved Searches) (see here)
  
• October 8: the bug seemed to be repaired (see here)
• October 15: another bug appears to be reintroduced: you can save relevant records in My Collections to run them later in PubMed. However, although the search is executed, it does not appear in the Search History.

For me this is an essential feature of My Collections.Often, when I develop a sensitive search, I collect all relevant studies, especially the ones that were not in my search (i.e. found by checking references or ‘related articles’). Then I optimize the search and hope all the relevant records will be found. This can be checked by combining (a) search(es) with the collection(s). If the search is good all relevant records will be found.

Of course this will only work when you CAN combine the collection from My NCBI with one or more searches in the History.

A cumbersome solution, that only works for one collection at the time, is that you send the collections (executed in PubMed) to the Clipboard and combine this set (#0) with the searches, but I prefer a simpler solution. In fact it has always been possible in the past….

Well we will write again to the help desk.
Hopefully I will report the bug repair next week and there will be no follow up.

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Voor de tweede keer een bug in My NCBI. Dit keer gaat het om “My Collections”. Als je een “collection” activeert, worden de desbetreffende records (in het voorbeeld 39 items) wel uitgevoerd in PubMed, maar komen ze niet in de History terecht.

Dat vind ik erg vervelend, omdat ik My Collections vooral gebruik om uitgebreide zoekacties op te zetten.

Ik sla alle relevante artikelen op in My Collections en voer ze op een later tijdstip uit. Dan combineer ik ze met een of meer searches. Ik kan zo checken of ik met zo’n search alle relevante artikelen (bijv. gekregen van klant of via related articles) vind. Is dat niet het geval, dan is het een manier om ontbrekende termen te vinden.

Deze procedure werkt nu dus niet meer, omdat een set uit My Collections niet in de History terechtkomt.

Ik heb wel een voorlopige kunstgreep bedacht, t.w. deze items in Pubmed naar het Clipboard sturen, zodat ze alsnog als set #0 in de History komen te staan. Dat werkt natuurlijk maar met 1 set tegelijk en is tamelijk omslachtig.

Voorheen werkte dit trouwens wel altijd, dus het zal wel weer liggen aan de overhaaste ‘reparaties’ en aanpassingen.

Nou, dat wordt weer een mailtje richting helpdesk.

Hopelijk wordt het snel verholpen en hoort u even niet meer van mij..