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

30 06 2009

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

28-6-2009 12-12-32 PubMed acute pancreatitis  sonder language restr

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.

28-6-2009 12-38-45 results acute pancreatitis kort 4 vd 28 its

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.

29-6-2009 2-58-03 NCBI acute pancreatitis

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)

29-6-2009 23-53-39 OMIM 12

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

30-6-2009 11-18-27 3x oMIM

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.

30-6-2009 1-06-47 SCM

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]

30-6-2009 2-02-47 save search

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

30-6-2009 2-45-29 myncbi2

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.

30-6-2009 4-05-06 details pcosSometimes 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)

30-6-2009 13-33-33 Clinical Queries

30-6-2009 13-41-52 SR spironolactoneYou 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).

29-6-2009 1-44-31 hand foot pubmedYou 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:

30-6-2009 14-17-36 foot arm history(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…

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Co-comment faster than light?

1 10 2008

Just a very short note on something I stumbled upon in co-comment.

As I wrote previousy (in Dutch) I use co-comment to keep track of my comments, comments to interesting items and comments to posts of my favorites.

Today I got a red envelope in my Firefox toolbar notifying me there was a new comment.

Looking at co-comment I saw my comment of 43 min ago at PIMM, Partial Immortalization. However when I took a look at his site the comment was still awaiting moderation.

I noticed this before when some-one else (Wowter) posted a comment at my site: that comment already showed up at my co-comment before I even read it, let alone approved it!

This is kind of odd: what is moderation worth if the the comment is already made public elsewhere?

Is this one of the reasons that there are so many double or triple entries of the same comment in Co-comment, one after placing the comment, the copies after approval or editing??

What about spam-comments?





Not another howto… but whetherto!

10 05 2008

Liked this: “Not another 8 ways” post from “Levite Chronicles”

While reading another HOW-TO book he reflects that he would rather need WHETHER-TO books/guides.

“How do I decide whether to take those steps, to read that book, to read the blog that mentions the book, to write this post rather than clean off the desk or make the bed or just stop and think?”

His refers to another statement, which makes sense to me:

What separates the great innovator from the mere data gatherer is the ability to stop gathering data and think about what has been gathered.” (from **CrazyBusy: Overstretched, Overbooked, and About to Snap! Strategies for Handling Your Fast-Paced Life, by Dr Edward Hallowell, p 132.).

Yes, I do think I need a whether-filter. Do you?





A really delicious blog …

8 05 2008

If you like food, blogging, excellent photography, recipes, information about Munich and Web technology and tools including WordPress plugins, than don’t miss delicious days.

In “about” you can read that “delicious days” is made by a passionate German couple in Munich.
She loves to cook and has a job in the design and internet business world and he learned to enjoy cooking and is the technical genius behind the site.

The blog is beautifully designed. Look for instance at the Gallery, with perfect photo’s sorted by category. After you have choosen a particular photo you can move to the next or previous ones or press the play button.

In the recipe-list you can get an idea of the recipe by pressing the “preview”-button, while remaining in the list.

food

Why do I refer to this blog here? I like food, that’s for sure, (I even have a web page on a dutch food web site, smulweb), but I came here while following a link from bakkel dot com (once again) to http://www.deliciousdays.com/cforms-plugin, which is in fact one part of the plugin pages/tabs at delicious days. You’re free to share these plug-ins.

***************************************************************

Als je gek op lekker eten bent, recepten, blogging, mooie foto’s, en geinteresseerd in web 2.0 trucjes zoals wordpress plugins neem dan eens een kijkje op de food blog delicious days.

Delicious days wordt gerund door een duits stel, waarvan zij de de liefde voor het eten heeft ingebracht en via haar werk kennis heeft van design en internet business, en hij de technische inbreng verzorgt. Een ideale mix.

Delicious days is een WordPress blog, maar zo aangepast in stijl dat dat niet direct opvalt. Het zit heel vernuftig in elkaar. In the Gallery kun je foto’s in een categorie individueel bekijken of in serie afspelen. In de receptenlijst kun je eerst een indruk krijgen van het recept door op “preview” te klikken, waardoor er een stijlvolle pop-up tevoorschijn komt. De wordpress-plugins die ze met je willen delen staan op een aparte pluginpagina.

Waarom ik op deze blog terecht kwam? Ik ben zelf een liefhebber van eten en ben geinteresseerd in voedsel in bredere zin; ik heb zelfs een eigen webpagina op smulweb), maar ik kwam toevallig op deze site door (wederom) een link te volgen via bakkel dot com naar cforms-plugin op deze site. Ook weet ik dat enkele spoetnikers zoals Moira geinteresseerd zijn in eten en aan een Google-doc over dit onderwerp hebben samengewerkt (ik weet uit mijn hoofd niet meer wie). Misschien hebben ze hier wat aan. Tevens zullen sommigen die graag zelf hun wordpress willen (gaan) hosten misschien wat hebben aan de tips en de plug-ins. Anderen zullen kunnen genieten van de foto’s.