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]
About these ads

Actions

Information

14 responses

26 11 2009
Tweets that mention Adding Methodological Filters to MyNCBI « Laika’s MedLibLog -- Topsy.com

[...] This post was mentioned on Twitter by Laika (Jacqueline), Ewa Dobrogowska. Ewa Dobrogowska said: Adding Methodological Filters to MyNCBI via: @laikas Thank you so much Jacqueline,I haven't known so much about MyNCBI: http://bit.ly/8zEr2v [...]

26 11 2009
Christian Sinclair

Awesome post. I can’t wait to try and enhance some of my pre-existing filters. Thanks for these posts on increasing the utility of PubMed. I don’t think a lot of physicians are even slightly familiar with some of the tools out there which once learned can make their lives so much easier.

26 11 2009
uberVU - social comments

Social comments and analytics for this post…

This post was mentioned on Twitter by Pudliszek: Adding Methodological Filters to MyNCBI via: @laikas Thank you so much Jacqueline,I haven’t known so much about MyNCBI: http://bit.ly/8zEr2v

14 12 2009
Social medias, web services and tips for health in MedLib’s Round 1.9 | Knowledge beyond words

[...] Adding Methodological Filters to MyNCBI posted at Laika’s MedLibLog by Jacqueline [...]

16 12 2009
NOT ONE RCT on Swine Flu or H1N1?! – Outrageous! « Laika’s MedLibLog

[...] repeated the search, and using prefab “My NCBI filters” for RCTs discussed before I get the following [...]

17 12 2009
MedLib’s Round 1.9 about social media and web services | Dr Shock MD PhD

[...] Adding Methodological Filters to MyNCBI posted at Laika’s MedLibLog by Jacqueline. Jacqueline has created a great tutorial to learn how to add methodological filters to MyNCBI. [...]

17 12 2009
Science Report » Blog Archive » MedLib’s Round 1.9 about social media and web services

[...] Adding Methodological Filters to MyNCBI posted at Laika’s MedLibLog by Jacqueline. Jacqueline has created a great tutorial to learn how to add methodological filters to MyNCBI. [...]

8 06 2010
PubMed versus Google Scholar for Retrieving Evidence « Laika's MedLibLog

[...] one is looking for RCT’s and doesn’t do an exhaustive search). (see previous posts 2, 3, [...]

5 07 2010
Adicione filtros metodológicos no PubMed « Portal Tuxauas

[...] Adicione filtros metodológicos no PubMed by marcusts on 04/07/2010 Blog com todas as orientações em inglês: Adding Methodological Filters to MyNCBI « Laika\’s MedLibLog. [...]

7 07 2010
Thoughts on the PubMed Clinical Queries Redesign « Laika's MedLibLog

[...] your personal NCBI account so that the filters show up each time you perform a search in PubMed ( this post describes how to do [...]

7 07 2010
Clinical queries & custom filters in PubMed « (the) health informaticist

[...] an absolute breeze. Fortunately I don’t have to describe how to add your own filters as Laika has already done such a good job of it (with screenshots and everything…), and you can now add up to 15 of your own favourite search [...]

23 07 2010
Clinical queries & custom filters in PubMed

[...] an absolute breeze. Fortunately I don’t have to describe how to add your own filters as Laika has already done such a good job of it (with screenshots and everything), and you can now add up to 15 of your own favourite search [...]

18 10 2010
Problems with Disappearing Set Numbers in PubMed’s Clinical Queries « Laika's MedLibLog

[...] to your personal NCBI account so that the filters show up each time you do a search in PubMed. This post describes how to do [...]

21 08 2011
PubMed’s Higher Sensitivity than OVID MEDLINE… & other Published Clichés. « Laika's MedLibLog

[...] types. These filters are based on one or more of the above-mentioned principles (see earlier posts here and here). Simple Methodological Filters can be found at the PubMed Clinical Queries. For instance [...]

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s




Follow

Get every new post delivered to your Inbox.

Join 610 other followers

%d bloggers like this: