Practicing Medicine in the Web 2.0 Era

29 01 2010

Many people don’t get Web 2.0 – and certainly not Medicine 2.0.

Just the other day a journalist asked me if the redesigned PubMed could be called PubMed 2.0.
I said: “well no….no… not at all” ….Web 2.0 is not merely tools or fancy looks, it is another way of producing and sharing information and new web tools facilitate that. It is not only simplicity, it is participation. PubMed has changed it looks, but it is not an interactive platform, where you can add or exchange information.

Well anyway, I probably didn’t succeed to explain in just a few sentences what Web 2.0 is and what it isn’t. For those that are unfamiliar with Web 2.0 and/or how it changes Medicine, I highly recommend the following presentation by Bertalan Mesko (of ScienceRoll and Webicina), who explains in a clear and nontechnical way what it is all about.

By the way Bertalan is a finalist with ScienceRoll in the 2009 Medical Weblog Awards (category Best Medical Technologies/Informatics Weblog). He could surely use your vote. (here you can vote in this category). You can see all Finalist here.

Reblog this post [with Zemanta]




Adding Methodological Filters to MyNCBI

26 11 2009

Idea: Arnold Leenders
Text: “Laika”

Methodological Search Filters can help to narrow down a search by enriching for studies with a certain study design or methodology. PubMed has build-in methodological filters, the so called Clinical Queries for domains (like therapy and diagnosis) and for evidence based papers (like theSystematic Review subset” in Pubmed). These searches are often useful to quickly find evidence on a topic or to perform a CAT (Critical Appraised Topic). More exhaustive searches require broader  filters not incorporated in PubMed. (See Search Filters. 1. An Introduction.).

The Redesign of PubMed has made it more difficult to apply Clinical Queries after a search has been optimized. You can still go directly to the clinical queries (on the front page) and fill in some terms, but we rather advise to build the strategy first, check the terms and combine your search with filters afterwards.

Suppose you would like to find out whether spironolactone effectively reduces hirsutism in a female with PCOS (see 10+ 1 Pubmed Tips for Residents and their Instructors, Tip 9). You first check that the main concepts hirsutism and spironactone are o.k. (i.e. they map automatically with the correct MeSH). Applying the clinical queries at this stage would require you to scroll down the page each time you use them.

Instead you can use filters in My NCBI for that purpose. My NCBI is your (free) personal space for saving searches, results, PubMed preferences, for creating automatic email alerts and for creating Search Filters.
The My NCBI-option is at the upper right of the PubMed page. You first have to create a free account.

To activate or create filters, go to [1] My NCBI and click on [2] Search Filters.

Since our purpose is to make filters for PubMed, choose [3] PubMed from the list of NCBI-databases.

Under Frequently Requested Filters you find the most popular Limit options. You can choose any of the optional filters for future use. This works faster than searching for the appropriate limit each time. You can for instance use the filter for humans to exclude animals studies.

The Filters we are going to use are under “Browse Filters”, Subcategory Properties….

….. under Clinical Queries (Domains, i.e. therapy) and Subsets (Systematic Review Filters)

You can choose any filter you like. I choose the Systematic Review Filter (under Subsets) and the Therapy/Narrow Filter under  Clinical Queries.

In addition you can add custom filters. For instance you might want to add a sensitive Cochrane RCT filter, if you perform broad searches. Click Custom Filters, give the filter a name and copy/paste the search string you want to use as filter.

Control via “Run Filter” if the Filter works (the number of hits are shown) and SAVE the filter.

Next you have to activate the filters you want to use. Note there is a limit of five 15 filters (including custom filters) that can be selected and listed in My Filters. [edited: July 5th, hattip Tanya Feddern-Bekcan]

Under  My Filters you now see the Filters you have chosen or created.

From now on I can use these filters to limit my search. So lets go to my original search in “Advanced Search”. Unfiltered, search #3 (hirsutism  AND spironolactone) has 197 hits.

When you click on the number of hits you arrive at the results page.
At the right are the filters with the number of results of your search combined with these filters (between brackets).

When you click at the Systematic Reviews link you see the 11 results, most of them very relevant. Filters (except the Custom Filters) can be appended to the search (and thus saved) by clicking the yellow + button.

Each time you do a search (and you’re logged in into My NCBI)  the filtered results are automatically shown at the right.

Clinical Queries zijn vaak handig als je evidence zoekt of een CAT (Critical Appraised Topic) maakt. In de nieuwe versie van PubMed zijn de Clinical Queries echter moeilijker te vinden. Daarom is het handig om bepaalde ‘Clinical Queries’ op te nemen in ‘My NCBI’. Deze queries bevinden zich onder Browse Filters (mogelijkheid onder Search Filters)

Het is ook mogelijk speciale zoekfilters te creëeren, zoals b.v. het Cochrane highly sensitive filter voor RCT’s. Dit kan onder Custom Filters.

Controleer wel via ‘Run Filter” of het filter werkt en sla het daarna op.

Daarna moet je het filter nog activeren door het hokje aan te vinken. Dus je zou alle filters van de ‘Clinical study category’ kunnen opnemen en deze afhankelijk van het domein van de vraag kunnen activeren.

Zo heb je altijd alle filters bij de hand. De resultaten worden automatisch getoond (aan de rechterkant).

Reblog this post [with Zemanta]




PubMed® Redesign [2] News, webcast

4 10 2009

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
Reblog this post [with Zemanta]




PubMed® Redesign is here… to try.

1 10 2009

30-9-2009 23-35-13 pubmed try the redisgned PubmedWe 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/)
  • Reblog this post [with Zemanta]





    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…





    LOL: NCBI ROFL

    28 06 2009

    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:

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

    mj

    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”.





    PubMed Changes at the Front Door

    1 04 2009

    pubmed-logoThis 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:

    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

    8 03 2009

    pubmed-logoAlmost 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.

    pubmed-motor-neuropathy-mesh-1

    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).

    pubmed-motor-neuropathy-search-1

    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.

    pubmed-motor-neuropathy-search-1b-details

    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.

    pubmed-motor-neuropathy-2

    pubmed-motor-neuropathy-2a

    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.

    gopubmed-neuropathy

    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:

    ovid-motor-neuropathy-1

    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.

    ovid-motor-neuropathy-2

    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.





    Another bug in My NCBI?

    15 10 2008

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

    ——————————————————

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

    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.

    —————————-

    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..





    Bug My NCBI repaired

    8 10 2008

    I’m pleased to announce that the bug in PubMed’s My NCBI, that I pointed out a week ago, has been repaired.

    For two weeks, since the update of My NCBI, searches comprised of setnumbers were incorrectly saved in My NCBI, thus literally as #1 AND #2, or in the example I gave as: #3 + RCT filter instead of: hirsutism and spironolactone (+ RCT-filter), which was the actual search behind it. (see Figures below)

    This was the response I just received from someone of the U.S.National Library of Medicine:

    “You can now save searches with search statement (aka History) numbers. Unfortunately, any that you recently created that didn’t work are not going to work, so please delete those.

    As part of the fix, we made some changes to how links for saved search names work in My NCBI. On the screen where you used to see “View Results,” use the search name to link to run the search in PubMed. The “Edit” link now takes you to where you can change the specs of the search. These changes are not yet finished. When we have things running normally we will provide more detailed information in our newsletter.

    Thank you for your patience.”

    I’ve checked it and it really works. Thank god it does. It is really an essential feature, especially for the unexperienced searcher: the (correct number of) brackets are automatically in the right positions.

    I’m also pleased with the way the saved searched are presented. It is far more logic that the search is executed when clicking at the underlined name (which looks like a link) and that you can edit where it says “edit”.

    I’m looking forward to the other enhancements.

    search was erroneously saved as (#3) AND ....

    Search is now saved as: (((hirsutism) AND (spironolactone) AND ....

    The old (wrong) and updated search in My NCBI (in the new layout)





    About “1 AND 2 = 3” in My NCBI

    1 10 2008

    The PubMed My NCBI feature has been updated. The navigation is entirely different and -in my view- less intuitive and more complex. The increased complexity may relate to the new features, some seeming rather unnecessary (filters), others looking promising: my bibliography, persistent cookies, no limit to the number of saved searches or collections per account (hurray!).

    You can find details about the My NCBI changes in the NLM-bulletin and in MyNCBI-help.

    For now, I just want to address one point, that hopefully is a “temporary error”.

    I noticed it last Friday, thought that it was just a technical error of the kind that frequently occurs these days in PubMed, but will be restored without any notice.

    But the mistake (?) is still there. It is about HOW PubMed searches are saved

    Before, if you combined two sets, say: “#1 AND #2”, set #3 would be created: #1 AND #2.
    If you would save #3 in My NCBI, you would save the entire search behind #1 AND #2, but now only the string “#1 AND #2” is saved. You can easily imagine that set numbers #1 AND #2 are only meaningful if #1 AND #2 are still present and the same as in the original search.
    A Dutch colleague just shouted out he got an error message when trying to execute a saved search. Set X was not recognized….

    Example.

    Suppose you want to find an answer to the following question: Is spironolactone useful (compared to cyproterone acetate for instance) to reduce hirsutism in women with PCOS?

    You search for:

    • hirsutism (#1) and spironolactone (#2) (checking that these are mapped to the appropriate MeSH using Details)
    • combine the two sets with AND.
    • Subsequently combine #3 with a narrow filter for the Therapy Domain (filter for RCT’s) in the Clinical Queries.
    • Set #4 (=#3 AND filter) gives 23 results.
    • You save set #4 in My NCBI.
    • But what happens:
      It is saved as #3 AND filter, not as: hirsutism AND spironolactone AND filter.
      Reexecuting the search if the original History is gone yields 0 results (or an erroneous result).

    Personally I can circumvent most problems, because I optimize my searches in Word (also nice as safeguard when the PubMed servers are overheated), but for most users this is an unnecessary extra step.

    I hope this bug (?, I hope it is a bug) is quickly restored by NLM.

    Please inform them by writing to the PubMed helpdesk (at the bottom of the PubMed front page). I will do the same.





    Finding assigned MeSH terms and more: PubReMiner

    24 09 2008

    Generally when searching PubMed I use both MeSH and textwords. If you already have some nice articles, either by performing a quick and dirty search or looking at the Related Articles or your colleague gave you one or two, then you can find the MeSH assigned to these papers by looking in citation format (see Fig). However going through a set of articles looking at all indexed terms takes quite some time and one doesn’t easily get an overview of the overall frequency of MeSH in a set of records.

    Therefore, Rachel Walden, asked first at Twitter and then at David Rothman’ site (see here):

    “What I’d like to do is to be able to enter the PMIDs of several citations and have the tool search MEDLINE via PubMed for the assigned MeSH terms, and return a single list of the terms used by any of the entered citations with a measurement of frequency. For example, if I input PMIDs 16234728, 15674923, and 17443536, the tool would return results telling me that 100% or 3 of 3 use the term “Catheters, Indwelling”, 2 of 3 use “Time Factors,” 1 of the 3 uses “Urination Disorders,” and so on. Although this example uses 3 PMIDs, I’d like to be able to input at least 10, just based on personal experience.”
    (PMID is the unique PubMed-identifier, by searching for the PMID you get one specific record.)

    The suggestions made by several people were summarized by David in another post (see here). The following 3rd-party PubMed/MEDLINE tools seemed most promising:

    Both give useful results. The layout- is very user-friendly.

    I tried my own sets of 20 PMIDs (from a systematic review search on “predictive models for in vitro fertilization”) and http://www.docmobi gave this result:


    This was the result when I selected: “primary terms only“. If I selected “include secondary terms” I would find female and pregnancy as well, but at rates of 175%. First I didn’t understand, but than I realized that pregnancy occurs as “Pregnancy” and as “Pregnancy Rate”, whereas female occurs as “Female” and as “Infertility, Female”. Therefore Pregnancy and Female can occur more than once as single words in one record (thus accounting for >100%). It is odd however, that important MeSH like Pregnancy and Female (which are really check tags, MeSH that should be assigned to each article that is about pregnancy or females) are not included in the primary list.

    Although useful and nicely presented I still not find this ideal:

    • Check tags are not in the list (with “primary terms only”)
    • Publication types and substance names are in neither list.
    • Subheadings are not included. For words not captured by a single MeSH, but by a combination of MeSH and subheadings this is especially important.
      For instance, there is no MeSH for EGFR-inhibitors, you have to use:
      Receptor, Epidermal Growth Factor/antagonists & inhibitors
    • Textwords are not included (not on Rachel’s wish list but on mine)
    • Personally I find the list so simple that I would have find the terms immediately myself.

    Coincidentally I found another 3rd party tool which does the job much better (I think): (PubMed) PubReminer, produced by Jan Koster at our hospital (AMC, Amsterdam). I looked at it, because my colleagues and I are going to discuss it today.

    This is the procedure I would recommend to find assigned MeSH and more, starting from PubMed (which is not absolutely required, because you can also search directly in PubReMiner)

    • Collect the PMID’s of the papers you want to analyze.
    • If you have selected the papers in PubMed (on the Clipboard, in My collections or in your search set) then Set the Display Tab on: UI List (Unique identifiers), and export these PMID to a textfile by choosing “to Text” from the Send to button. You get a simple list of PMID’s that you can copy/paste to PubReMiner. (not required, but handy)

    • Go to PubReminer, paste the PMID’s in the search box as one string.
    • Click: “Start PubReminer” (if you enter a search you may wish to apply limits)

    • You see the results, in the following columns: Year, Author, Journal, (Text)Word, MeSH, Substance, Country.

    • Afterwards you can decide
      – Whether the words are searched in title only, in Title and Abstract or also in MeSH and RN.
      – which columns are displayed
      – whether similar words are merged or not.
    • You can use selected terms to build up your search in PubReMiner and/or
    • You can export the terms as a text-file (!)
    • And, by the way, you can download a plugin for IE or Firefox (Fig. right)

    This tool is not very intuitive, but the result is quite ideal.

    You get both a list of MeSH plus their subheadings AND a list of textwords (and substance names).

    There are very useful terms in here, for instance logistic models[mesh]. As textwords I should use ‘logistic regression’ or ‘multivariate analysis’. It is only a pity that terms are given individually and spread: the context is lost (‘analysis’ may for instance be too broad, it is only useful in combination with ‘multivariate’ or ‘regression’).
    With respect to the MeSH only individual terms are given. ‘Pregnancy’ is mentioned 19 out of 20 times in the MeSH-list. Does this mean I’m missing one paper by searching “Pregnancy”[MesH]? No, because that paper is indexed with the narrower term “Pregnancy Rate”. (and you will find it by exploding Pregnancy).
    So the context and the hierarchy are lost here as well.

    But it is about as good as one can get.

    I’m gonna use this tool (as an adjunct at least). Seems that it has some other potentials as well: look up genes, find the research interest of an author, determine the journal to submit your work to. Well I probably learn that in a few hours. Perhaps I will come back to it later.





    PubMed Search Clinic on ATM, Citation Sensor, Advanced Search: Video available.

    21 07 2008

    The video from the online Search clinic on recent PubMed changes, announced in a previous post is now available at: nlm.nih.gov (pmupdate08): click here.

    Direct link to the video only: https://webmeeting.nih.gov/p91519064/

    A good coverage is given by Michelle Kraft (Krafty Librarian) at her site (click here).

    The clinic, presented by Katherine Majewski, updated recent changes to PubMed, earlier described at the NLM information bulletins on the new ATM and the Beta Advanced Search page.
    Recent changes have also been amply described (and discussed) at several of my previous posts, most notably this one.

    Here is an overview, with emphasis on new aspects (at least to me).

    Citation Sensor:

    In the clinic the citation sensor was defined as: “a new feature designed for users seeking specific citations”. However it is not a separate search box. The citation sensor works automatically when you type words into the general search bar. If combination of words are recognized as representing citations (e.g. volume numbers, author names, journal titles) the matches are displayed in a yellow box above the retrieval.

    In my previous post I already discussed that the sensor doesn’t always work perfectly and like Krafty, I think that the Single Citation Matcher (in the blue side bar) performs better. It suggests author and journal titles as you write them. Furthermore, you can just fill in the specific information you know in specific fields, i.e. if the author name is misspelled/wrong, it often suffices to fill in year, page number and title word(s), to name just one possible combination. In response to a question, Majewski said the sensor is not an advantage per se as opposed to the Single Citation Matcher. Probably it is just handy for people used to a Google-like way of searching.

    One thing new to me was that there are two “Details” when performing a search.

    When you type: choi blood 2008, the citation sensor finds 6 hits, 3 of them shown in the yellow box.
    The Details button shows: choi[All Fields] AND (“blood”[Subheading] OR “blood”[All Fields] OR “blood”[MeSH Terms]) AND 2008[All Fields].

    However when you click 6 articles to see them all, the Details button shows how the citation sensor has translated the search in: choi[Author] AND (blood[Author] OR “Blood”[Journal]) AND 2008[Publication Date]

    Thus in fact the search is translated twice (although the citation sensor-results are always a subset of the full results). If you click on 6 articles, the 2nd translation appears as a 2nd search in the Search History.

    ATM – Automatic Term Mapping.

    ATM has been changed in conjunction with the citation sensor in order to identify queries that contain citation-type information. The old ATM mapped search terms to subject, journal, and author tables in that order. If a MeSH-match was found, PubMed would search for that MeSH as well the user-input as a textword (title, abstract). Automatic term mapping would then stop because it found a match with MeSH. Thus terms that are not only in the MeSH but also in the author or journal table would have been missed, such as in Burns Laryngoscope 2005. The old ATM would map Burns and Laryngoscope as MeSH (subject-search), but the new ATM also searches these terms in ‘all fields’, thus enabling the retrieval of the paper of Burns in Laryngoscope.
    In the Q & A part of the session Majewski advised to use qualifiers as MeSH when Burns is searched just as a topic. I only wonder if/how most of the untrained people would find this out.

    Another consequence, not really addressed here, is that multi-term words are split and searched individually. With the new ATM, gene therapy is not only searched as the phrase gene therapy (as MeSH-term and textword) but also as ”gene”[All Fields] AND “therapy”[All Fields], which leads to a far greater retrieval (almost 250%). Few of these extra hits are relevant. (see previous post)

    Statistics, however, show that the thousands (‘real’) queries performed returned only 10% extra hits on average (see ATM-FAQ for more information). According to NLM, the enhanced ATM and citation sensor have considerably improved searching PubMed. Probably because most people just come to PubMed to search a specific paper or subject (running one or two search commands). The new features enhance citation searches, while subject searches do not suffer too much as long as multiple terms (concepts) are used, as this will filter much of the noise seen with one term (because the term is searched within the context of the other word).

    My remark that most of my patrons do do subject searches was interpreted as “do do broad searches“. Which in effect they do (i.e. searches for systematic reviews), but I do not think the suggested NCBI books might be very helpful to them, although it might indeed serve those people (patients?) that want information about broad subjects like “burns”. Perhaps PubMed/NCBI can offer subject searchers other tools as well.

    Notably, based on user input there are now (as of July 2nd) some exceptions to the new ATM-rule:
    Substance names (such as ferrous glucanate) and
    MeSH with stand alone letters or numbers (like complement factor B) will not be broken apart, but searched as a phrase.

    Advanced Search (Beta-version)
    Advanced Search is amply discussed in a previous post. However, I didn’t mention that the page consists of 4 collapsible boxes beneath the Search Bar (I missed this: you have to click a small minus sign at the upper left of each box in order to collapse.) In essence you can search by many fields, the default fields displayed being Author, Journal, and Publication Date (box2) and all fields (box 4). There is an index for each selected field available (little buttons right of the search boxes). I see no other difference between box 2 and 4 than the defaulted field and the fact that you can only make multiple choices from the index in box 4. Answering a question in the audience Majewski said they might consider allowing multiple choices in box 2 as well.
    Box 3 shows limit-options, much the same as the Limit-tab in the usual frontpage, except that you can unlock your limits to future searches using the lock icon (by defaulted limits are carried to future searches).

    Thus again this new ‘enhancement’ mainly facilitates citation searches, not subject searches. Clinical Queries are absent and it is for instance not possible to look up any MeSH other than by index, and even this often goes wrong with multi-word terms. The question why MeSH-trees were unavailable in the beta-version remained unanswered at the clinic.
    It was a relief though to hear that there were no intentions to replace the normal PubMed frontpage by this advanced search page in due course.

    Katherine Majewski ended the clinic by saying that answers to the questions posed during the clinic would be shown at this NLM-page later. She also encouraged to give positive and negative feecback by writing to the NLM customer service and to be as specific as possible if your search was negatively affected by the recent PubMed changes.

    ——————————-

    NL flag NL vlag

    De video van de PubMed Search Clinic, die ik in een eerder bericht aankondigde is nu te zien op: http://www.nlm.nih.gov/bsd/disted/clinics/pmupdate08.html.

    Directe link naar de video: klik hier

    Michelle Kraft (Krafty Librarian) heeft de clinic al goed op haar blog samengevat.

    De webpresentatie, gegeven door Katherine Majewski, behandelde de recente PubMed-veranderingen, zoals aangekondigd in de NLM informatiebulletins (gewijzigde ATM-mapping resp. Beta Advanced Search)
    Eerder heb ik deze veranderingen ook al uitgebreid beschreven en becommentarieerd. (zie bijv. hier).

    Hier een samenvatting, met nadruk op nieuwe aspecten

    Citation Sensor:

    In de webpresentatie werd de “citation sensor” omschreven als: “a new feature designed for users seeking specific citations”. Het is echter geen aparte zoekoptie. De citation sensor doet zijn werk automatisch als je woorden in de algemene zoekbalk typt. De als citaties herkende hits worden apart op een gele achtergrond getoond.

    Eerder heb ik al opgemerkt dat de sensor niet altijd goed werkt en evenals Krafty denk ik dat de Single Citation Matcher (in the blauwe balk) veel beter werkt. Deze geeft nl. woordsuggesties terwijl je typt en je kunt elke mogelijke informatie specifiek invullen. Weet je een auteur niet dan kun je vaak volstaan met jaar, paginanummer en titelwoorden, om maar één combinatie te noemen. Volgens Majewski is de sensor ook niet perse beter. Waarschijnlijk is het vooral handig voor mensen die gewend zijn aan een Google-zoekwijze en die verder weinig weten van PubMed. Zelf zou ik toch wel graag willen dat je de citation sensor naar believen aan of uit kon zetten.

    Ik zag nu pas voor het eerst dat je 2 “Details” hebt, als de citatie-sensor iets mapt.

    Typ je: choi blood 2008, dan vindt de sensor 6 hits en toont er 3.
    Onder Details is te zien dat Pubmed de search vertaald als: choi[All Fields] AND (“blood”[Subheading] OR “blood”[All Fields] OR “blood”[MeSH Terms]) AND 2008[All Fields].

    Als je op 6 articles klikt om ze allemaal te zien, staat onder Details hoe de citatie-sensor de search vertaald heeft: choi[Author] AND (blood[Author] OR “Blood”[Journal]) AND 2008[Publication Date]

    Dus, er zijn eigenlijk 2 ‘vertaalslagen’ Als je op 6 articles klikt dan verschijnt de 2e mapping als een zoekset in the zoekgeschiedenis.


    ATM – Automatic Term Mapping.

    ATM is evenals de citatie-sensor ontwikkeld aangepast om zoekacties gericht op het vinden van artikelen te vergemakkelijken. De oude ATM stopte met het zoeken van termen in de MeSH-, auteurs- en tijdschriftenlijst als een passende MeSH was gevonden. Tevens werd het ingetypte woord als tekstwoord gezocht. Met als gevolg dat termen die zowel in de MeSH- als in de auteurs- of tijdschriftenlijst voorkwamen nooit anders dan als MeSH (en tekstwoord) werden gezocht. Met Burns Laryngoscope 2005 zou dus nooit het artikel van Burns in Laryngoscope zijn gevonden. Met de nieuwe ATM lukt dat wel.
    Majewski adviseerde om veldenaanduidingen (qualifiers). zoals MeSH te gebruikenals je op een onder onderwerp zoals ‘Burns’ wilt zoeken. Dan vraag je je wel af in hoeverre de gemiddelde Pubmed -gebruiker dit weet.

    Tijdens de sessie werd niet echt aangekaart dat termen die uit meerdere woorden bestaan worden opgesplitst en in alle velden worden gezocht. Eerder heb ik al laten zien dat bij de nieuwe ATM 2,5 x meer hits oplevert met een term als gen therapie en dat de meeste van deze hits weinig relevant zijn.

    Volgens de NLM statistieken leiden echte zoekacties gemiddels slechts to 10% extra hits (zie ATM-FAQ voor meer info) en zijn zoekacties door de vernieuwingen aanzienlijk verbeterd . Waarschijnlijk omdat de meeste mensen alleen maar snel even iets opzoeken (1-2 zoekopdrachten) en vooral geinteresseerd zijn in specifieke artikelen. Wat dat levert het intypen van wat termen in de zoekbalk nu eerder wat op, en zolang je veel termen met elkaar combineert heb ik ook niet veel last van veel ruis bij het zoeken op onderwerp. Maar ik ben zeker niet overtuigd dat dit het zoeken op onderwerp verbetert.

    Mijn opmerking dat mijn klanten vooral op onderwerp zoeken werd opgevat als dat ze vooral breed zoeken. Nu is dat wel zo, maar ik denk niet dat zij veel aan suggesties hebben als NCBI-books. Dit lijkt me wel geschikt voor mensen die zich globaal willen inlezen in een onderwerp als brandwonden (burns), patienten bijvoorbeeld. Misschien heeft PubMed/NCBI wel nog andere tools voor uitputtende searches in het verschiet….

    Op basis van gebruikersfeedback zijn er vanaf 2 Juli wel enkele uitzonderingen op de nieuwe ATM-regel, t.w.:
    Substance names (zoals ferrous glucanate) en
    MeSH with losstaande letters en cijfers worden niet langer opgesplitst, maar als phrase gezocht.

    Advanced Search (Beta-versie)
    Advanced Search heb ik ook eerder uitgebreid besproken (zie hier). Wat ik nu pas bemerk, is dat de velden onder de zoekregel in-en uitklapbaar zijn. Er is een miniscuul min tekentje helemaal linksboven elk veld, waar je op moet klikken om het veld te verkleinen.

    De essentie van advanced search is dat je veel verschillende velden kunt doorzoeken, maar dat de standaard velden weer citatie-gericht zijn, dus: Author, Journal, and Publication Date (veld 2) en All Fields (veld 4). Je kunt termen voor elk gekozen veld opzoeken in een index (klein knopje rechts). Ik zie eigenlijk geen verschil tussen veld 2 en 4, behalve dan het standaard veld en het feit dat je in het 4e veld verschillende termen tegelijk kunt aanklikken. Mogelijk komt deze optie ook voor veld 2.
    In veld 3 kun je limieten aanklikken, eigenlijk erg vergelijkbaar met de Limit-Tab op de PubMed openingspagina. Wel prettig dat je een limiet desgewenst alleen gedurende één zoekactie kunt toepassen (default: blijft alle zoekacties aanstaan).

    Dus ook advanced search beta is vooral ten dienste van degene die bepaalde artikelen zoekt. Je kunt bijvoorbeeld alleen maar de MeSH in de index opzoeken en er zijn geen Clinical Queries. De vraag waarom De MeSH-hierarchie niet geraagdpleegd kon worden vanuit bleef onbeantwoord.
    Het was wel een pak van mijn hart, dat het volgens Majewski niet de bedoeling was dat de Advanced Search de normale openingspagina op termijn zou vervangen.

    Katherine Majewski beeindigde de sessie met de mededeling dat antwoorden op gestelde vragen later op deze pagina zou verschijnen.

    Ze verzocht iedereen ook hun eventuele problemen met de veranderingen zo specifiek mogelijk aan de help desk door te geven.





    PubMed Online Search Clinic on ATM!

    17 07 2008

    Just a short note at the last moment.

    Back from vacation I picked up some twitter and blog messages announcing a PubMed search clinic offered at July 17 (today!) at 2pm Eastern time (8pm Amsterdam/Paris time, see timetable throughout the world).

    A 30 minute online search clinic will be presented by the NLM® and the National Training Center and Clearinghouse (NTCC) via Adobe® ConnectTM on Thursday, July 17th (2pm ET). The presentation will cover changes to PubMed including changes to how PubMed handles your search (the new automatic term mapping process), the citation sensor, and the beta Advanced Search page.

    There is a maximum capacity of 300 participants, on a first come first served base. However, the clinic will be recorded and will be available for viewing later.

    To follow the clinic log in at: https://webmeeting.nih.gov/pmupdate08/

    or: http://www.nlm.nih.gov/bsd/disted/clinics/pmupdate08.html.
    Here you find more info about the clinic, as well as tips for successful participation in the clinic. Be sure to test it beforehand.

    Sources:

    The Krafty Librarian: @Krafty (twitter) and several posts on her blog.

    Nikki (Eagledawgs) guest post on David Rothman’s blog

    Background info on what others have blogged about recent Pubmed can be found on another Krafty Librarian’s post and several of my previous post, including PubMed: Past, Present And Future, PART II

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

    Even op de valreep.

    Net terug van vakantie zag ik enkele twitters en blogberichten die een “PubMed search clinic” aankondigden.

    Deze begint om 8 hr p.m. (welke tijd waar?).

    Het duurt 30 minuten en gaat over de recente veranderingen in Pubmed, de nieuwe ATM (automatic term mapping), de citation sensor en Advanced Search Beta.

    Er kunnen 300 mensen deelnemen, volgens het “wie het eerst komt, het eerst maalt” principe. De clinic wordt wel opgenomen, zodat je hem later nog eens kunt bekijken.

    Inloggen voor 19.00: https://webmeeting.nih.gov/pmupdate08/

    Meer info op: http://www.nlm.nih.gov/bsd/disted/clinics/pmupdate08.html.
    Inclusief tips om de clinic goed te kunnen volgen.

    Bronnen:

    The Krafty Librarian: @Krafty (twitter) en verschillende blogberichten.

    Nikki (Eagledawgs) te gast op het blog van David Rothman.

    Achtergrondinfo over wat anderen van de veranderingen vinden zijn ook te vinden de site van Krafty Librarian (zie hier). Enkele van mijn eerdere berichten zoals PubMed: Past, Present And Future, PART II zijn er ook aan gewijd.