Thoughts on the PubMed Clinical Queries Redesign

7 07 2010

Added 2010-07-09:  It is possible to enter the set numbers again, but the results are not yet reliable. They are probably working on it.

Last Wednesday (June 30th 2010) the PubMed Clinical Queries were redesigned.

Clinical Queries are prefab search filters that enable you to find aggregate evidence (Systematic Reviews-filter) or articles in a certain domain (Clinical study category-filters: like diagnosis and therapy), as well as papers in the field of  Medical Genetics (not shown below).

This was how it looked:

Since there were several different boxes you had to re-enter your search each time you tried another filter.

Now the Clinical Queries page has been reconfigured with columns to preview the first five citations of the results for all three research areas.

So this is how it looks now (search= PCOS spironolactone cyproterone hirsutism (PubMed automatically connects with “AND”))

Click to enlarge

Most quick responses to the change are “Neat”, “improved”, “tightened up”…….

This change might be a stylistic improvement for those who are used to enter words in the clinical queries without optimizing the search. At least you see “what you get”, you can preview the results of 3 filters, and you can still see “all” results by clicking on “see all”.  However, if you want to see the all results of another filter, you still have to go back to the clinical queries again.

But… I was not pleased to notice that it is no longer possible to enter a set number (i.e. #9) in the clinical queries search bar.

….Especially since the actual change was just before the start of an EBM-search session. I totally relied on this feature….

  1. Laika (Jacqueline)
    laikas Holy shit. #Pubmed altered the clinical queries, so that I can’t optimize my search first and enter the setnumber in the clin queries later.
  2. Laika (Jacqueline)
    laikas Holy shit 2 And I have a search class in 15 minutes. Can’t prepare changes. I hate this #pubmed #fail
  3. Mark MacEachern
    markmac perfect timing (for an intrface chnge) RT @laikas Holy shit 2 And I have a search class in 15 min. Can’t prepare changes. #pubmed #fail

this quote was brought to you by quoteurl

Furthermore the clinical study category is now default on “therapy broad” instead of narrow. This means a lot more noise: the broad filter searches for (all) clinical trials, while the narrow filter is meant to find randomized controlled trials only.

Normally I optimize the search first before entering the final search set number into the clinical queries.(see  Tip 9 of  “10+1 Pubmed tips for residents and their instructors“).  For instance, the above search would not include PCOS (which doesn’t map to the proper MeSH and isn’t required) and cyproterone, but would consist of hirsutism AND spironolactone (both mapping to the appropriate MeSH).

The set number of the “optimized” search is then entered in the search box of the Systematic Review filter. This yields 9 more hits, including Cochrane systematic reviews. The narrow therapy filter gives more hits, that are more relevant as well (24).

The example that is shown in the NLM technical bulletin (dementia stroke) yields 142 systematic reviews and 1318 individual trials of which only the 5 most recent trials are shown. Not very helpful to doctors and scientists, IMHO.

Anyway, we “lost” a (roundabout) way- to optimize the search before entering it into the search box.

The preview of 3 boxes is o.k., the looks are o.k. but why is this functionality lost?

For the moment I decided to teach my class another option that I use myself: adding clinical queries to your personal NCBI account so that the filters show up each time you perform a search in PubMed ( this post describes how to do it).

It only takes some time to make NCBI accounts and to explain the procedure to the class, time you would like to save for the searches themselves  (in a 1-2 hr workshop). But it is the most practical solution.

We notified PubMed, but it is not clear whether they plan to restore this function.

Note: 2010-07-09:  It is possible to enter the set numbers again, but the results are not yet reliable. They are probably working on it.

Still, for advanced users, adding filters to your NCBI may be most practical.

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*re-entering spironolactone and hirsutism in the clinical queries is doable here, but often the search is more complex and different per filter. For instance I might add a third concept when looking for an individual trial.

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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).

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PeRSSonalized Medicine – and its alternatives

27 02 2009

perssonalized_medicineA few posts back I just discussed that Personalized Genetics has not fulfilled its promise yet. But what about PeRSSonalized Medicine, just launched by Bertalan Mesko?

Bertalan Meskó is a medical student from Hungary, who runs the award-winning medical blog Scienceroll. According to the web 2.0 model of Hugh Carpenter, mentioned in a previous post, Bertalan (Berci) just finished his journey as a Web 2.0 jedi: he started a web 2.0 company: Webicina. Webicina offers a personalized set of web 2.0 tools to help medical professionals and patients enter the web 2.0 world.

To be honest I was a bit skeptical at first. When I think of web 2.0, I think of it as *open, *collaborative, *creative commons, *networking, ****collective intelligence (Elizabeth Koch). Web 2.0 exists by the mere fact that people want to share information for free. Later I realized that this initiative is comparable to individualized courses that you have to pay for as well. Webicina will also offer some free tools, especially for patients.

One such free tool is PeRSSonalized Medicine. The RSS in PeRSSonalized Medicine stands for Real Simple Syndication, which is a format for delivering regularly changing web content, i.e. from Journals. PeRSSonalized Medicine is a free tool meant to help those users who cannot spend much time online (e.g. medical professionals). It helps them track medical journals, blogs, news and web 2.0 services really easily and creates one personalized place where they can follow international medical content without having a clue what RSS is about (see post at Scienceroll)

persssonalized-medicine-tabs

PeRSSonalized Medicine has a beautiful and straightforward interface. There are 5 separate sources you can follow: (1) Medical Journals, (2) Blogs, (3) News and (4) Media (including Youtube channels, Friendfeed rooms or Del.icio.us tags), and (5) “articles” in PubMed (to setup this you have to perform a search in a separate toolbar).

The items included are partly of general interest -i.e. the Medical Journals includes 13 titles, including the BMJ, the JAMA and the Lancet-, partly it is very specialized, i.e. on the field of genetics. A lot of Journals are not included and Web 2.0 sources tend to be more represented than the official media/journals.Thus this tool seems most suited for the generalist and people wanting to follow web 2.0 tools. On the other hand – and this is a clear advantage- the content develops as wishes and suggestions are taken into account.

Each Tab can be personalized by simply hiding the titles you don’t want to include (under the button personalize it), but settings are only saved after registration.

The view of the personalized page is pleasant and neat. You see short titles of the 10 latest articles of the sources you have subscribed to. Moving your mouse over the titles will reveal more information and once you clicked the link it turns grey instead of blue. What I miss is the button: more, so you can catch up if you have missed older articles. Especially with media and journals that often have more than 10 new articles per issue, even more so if the first 10 titles consist of “obituaries” (BMJ).

The latest addition to PeRSSonalized Medicine (5) is the possibility to subscribe to a Pubmed search so “you can also follow the latest articles in your field of interest without going back to PubMed again and again and doing a search for your favourite term. Make this process automatic with PeRSSonalized Medicine.”
However, as most of you may know, you don’t have to go back to Pubmed over and over again to “do” your search, but you can easily subscribe to a search in PubMed either by email (My NCBI) or by RSS (see for instance this post in Dutch). Although the process of subscribing is not as intuitive as it is in PeRSSonalized medicine, PubMed is better suited to design a good search strategy. To keep abreast of the latest information in your field a good search forms the basis. It hurts my heart as a librarian that most web 2.0 people are more fixed on the technique of how to subscribe to a feed (RSS) than on good search results. Remember, it still is: garbage in, garbage out. RSS is just the drain.

As an example I show two RSS feeds below, one with more appropriate terms (pulmonary embolism and d-dimer) than the other (lung embolism and d-dimer). Pulmonary embolism is a MeSH. It is evident that with lung embolism articles will be missed just by choosing wrong/less optimal terms.

pubmed-search-rss-toelichting

Again the presentation of results is pleasant. Apart from the search restrictions I don’t find it very handy to look up each paper in HubMed (for that is where the link takes you).
Personally I prefer regular e-mail-alerts at specific intervals (via MyNCBI). I would like to look up citations either individually (if there is just 1 interesting hit) or all at once (10-50 hits). In PubMed, results can be selected, PDF’s directly downloaded from the library website and citations can be kept in My NCBI Collections or imported into a reference manager system. A RSS-feed of Pubmed searches is also handy (see below).

Alternatives

The idea presented on Webicina, although fancy, is not new. Consider the following alternative web tools, also build on data collected from RSS feeds.

Amedeo

Amedeo is dedicated to the free dissemination of medical knowledge. It is an international free service that will send you weekly literature updates in medical subjects of your choosing. At the same time a personalized website is made, with subscriptions to the journals you selected. You can retrieve the articles in text or in HTML-format. The HTML format brings you to the latest results for that Journal in PubMed. This service seems most suitable for specific medical disciplines. General topics (family physician) are not available, although it is possible to subscribe to for instance the American Journal of Family Physicians. As with all these free literature services, you will have to subscribe. It is easy to select or deselect journals in a category (tick boxes).
Amedeo also has Free Books For Doctors, but no podcasts or blogs. You can search the site, but you cannot easily look up individual journals.

amadeo

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emergency-medicine-2x

MedWorm (and LibWorm)

MedWorm is a free medical RSS feed provider as well a a search engine. It is meant both for doctor and patient. There are many medical categories that you can subscribe to, via the free MedWorm online service, or another RSS reader of your choice, such as Google Reader. The number of RSS-feeds is enormous: >6000. There are a publications directory, a blog directory, a blog tag cloud, consumer health news, discussion and several specific topics, like cancers, drugs, vaccines and education. Within the publications directory there is a further subdivision in: Consumer – Info – Journals – News – Organizations – Podcasts.

Many specialties are represented, including primary care and veterinary science. I tried it out and subscribed to some Addison’s disease related topics, Reuter’s Health and my own blog, which has recently been included. When you subcribe via the Medworm-RSS all news can be read in “My River of News”. It shows the titles and part of the abstracts (see Fig. below).

You can subscribe to single items or categories, but it is not possible to in- and exclude individual feeds within a topic or category by a single action. So within Endocrinology I cannot selectively exclude all diabetes journals, but (as far as I can see) I have to subscribe to each individual journal, if I don’t want the whole package. The loading of the River of News takes long, sometimes.

Together with David Rothman the builder/owner of MedWorm, Frankie Dolan, has also launched Libworm, which is a librarian’s version of MedWorm.

medworm2-home-page-favs

DO IT YOURSELF (or let the library do it for you)

Sometimes the library will set up a personalized start page. See for instance the Dermatology page created with Netvibes at the Central Medical Library, University Medical Center Groningen (UMCG). Doesn’t it look beautiful?

groningen-dermatology-netvibes

I-Google

And isn’t the tool below superb looking? Well, I constructed it myself on basis of what Ves Dimov wrote in the post “Make Your Own “Medical Journal” with iGoogle Personalized Page”, he submitted to the first MedLib”s round. And I had a little “life” help from Ves via Twitter, because things have changed a bit. All you need is a free Google mail (G-mail) account, just go to Google.com/IG (or search the web for I-Google) and subscribe. First you can create your start page with all kind of gadgets (like clock, G-mail inbox and weather forecast, see Figure below) and then you can add other tabs (encircled below). The Medical Journal and Journals Tabs I just took from Ves by clicking on the links he gave in his post: RSS feeds of the “Big Five” medical journals (NEJM, JAMA, BMJ, Lancet and Annals) plus 2-3 subpecialty journals and the podcasts of 4 major medical journals in iGoogle.

Once you have these tabs you can edit them (add, delete, move) as you like.

i-google

I-Google Medical Journals Tab

i-google-start-page-shape-top

I-Google Startpage

RSS-readers

All the above tools are based on RSS, which means Real Simple Syndication. It isn’t called Simple for nothing. You can easily do it yourself, which means that you have more freedom in what you subscribe to. Because I-Google doesn’t scale well beyond 50 or so RSS feeds, other RSS-readers are advisable once you subscribe to many different feeds (see Wikipedia for list and comparison) . I use Google-Reader, shown below, for this purpose.

Generally, adding Feeds is easy. In Firefox you often see the orange RSS-logo in the web browser (just click on it to add the feed) and most Journals and blogs have a RSS-button on their page, that enables subscription to their feed.

google-reader

rss-buttons-at-site-in-browser

As detailed in another (Dutch) Post, numerous Pubmed searches can be easily added to your RSS-reader. You build up a good search in Pubmed, for instance: (pulmonary embolism[mh] OR pulmonary embolism* OR lung embolism*) AND (“Fibrin Fibrinogen Degradation Products”[Mesh] OR d-dimer). In “the Results” you click on “Send To” and choose RSS-Feed and add it to your reader. That’s all.

pubmed-rss

Summary

PeRSSonalized Medicine is a free tool which lets you subscribe to a small and rather skewed selection of journals, news, media and blogs and (straightforward) PubMed searches. The strong points of this tool are: the beautiful design, the ease of use for people not used to web 2.0 tools including RSS, and its continuous development, seeking active input from its users. To speak with dr Shock’s: It is meant for a physician who is not web savvy, never heard of RSS and never wants to, not a geek, nerd, and still wants to stay up to date with health 2.0 or medicine 2.0.”

But there are other free tools around with more (subscription) possibilities and with a little more investment of time you can do it yourself and make subscriptions really perssonalized. Once you know it is simple, believe me.

You may also want to read:

https://laikaspoetnik.wordpress.com/2008/05/05/1-may-rss-day/ (about RSS)

https://laikaspoetnik.wordpress.com/2008/02/15/rss-feed-en-pubmed/ (about RSS and Pubmed – Dutch)





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.