PubMed custom filters: where the bee sucks

Work without Hope draws nectar in a sieve,
And Hope without an object cannot live.
~  Samuel Taylor Coleridge

bee-sucksI received a prompt comment from the programmer responsible for the new custom filter feature in My NCBI. I was assured that any bugs are now being corrected. Reason for hope.

I was also told that my health literacy filter was broken. It had somehow accumulated a few of those annoying smart quotes (subject for another rant at another time). I carefully retyped all the quotation marks. But the filter still doesn’t work properly. Although it tells me how many records I will find, it won’t apply the filter when I click the tab. I have to copy the code into the search box myself.

However, I did have luck with other attempts at custom filtering. I am frequently asked for Canadian content from PubMed. So I created a simple search and saved it in Custom Filters. Here is the code:

“canada”[MeSH Terms] OR canad*[All Fields]

Sidebar. You’d think that “canad*[All Fields]” would be sufficient, but that search produces fewer results than when ORing the two terms above.

Having added the new filter to my tabs, I did a general PubMed search on “diabetes.” I clicked my Canada tab and it worked. PubMed instantly created a subset, just as if I had ANDed the code to “diabetes” in the search box. From 330,831 records I was able to limit to 7,470 records with some mention of Canada. I love it, but not unconditionally.

What a pity that, as reported in the NLM Technical Bulletin of May 29, custom filters do not have the “tack” on the filter name tab – which means you can’t further refine your results by, say, clicking on the “Published in the last 5 years” tab.

It occurred to me that the Custom Filters feature might be having trouble with very long strings of code. I experimented with the Cochrane filter for controlled trials (see Robinson et al. Int J Epidemiol. 2002 Feb;31(1):150-3.) True nectar to the professional:

(randomized controlled trial[pt] OR controlled clinical trial[pt] OR randomized controlled trials[mh] OR random allocation[mh] OR double-blind method[mh] OR single-blind method[mh] OR clinical trial[pt] OR clinical trials[mh] OR (“clinical trial”[tw]) OR ((singl*[tw] OR doubl*[tw] OR trebl*[tw] OR tripl*[tw]) AND (mask*[tw] OR blind*[tw])) OR (“latin square”[tw]) OR placebos[mh] OR placebo*[tw] OR random*[tw] OR research design[mh:noexp] OR comparative study[mh] OR evaluation studies[mh] OR follow-up studies[mh] OR prospective studies[mh] OR cross-over studies[mh] OR control*[tw] OR prospectiv*[tw] OR volunteer*[tw]) NOT (animal[mh] NOT human[mh])

Plug this un-in-one-breath-utterable cryptogram into Custom Filters and it works perfectly. WTMI. Whom the Gods would destroy, etc.

I must apologize for the flippant remarks I made in my previous post. It must have been the nicotine. I hope that the snag with the NLM health literacy filter can be fixed. I intend to use Custom Filters frequently and uncomplainingly when all the kinks are worked out. Can we then look forward to the addition of the kitschy tack icon to the custom filter tab? That would be nectar indeed.

Where the bee sucks, there suck I.

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2 Responses to “PubMed custom filters: where the bee sucks”


  1. 1 a user June 13, 2009 at 1:23 am

    Don’t worry, we all understand the frustration of tools that don’t work (thinking about Microsoft Internet Explorer as I type this…).

    It would be great if you also left a comment for the NLM on that Health Literacy page letting them know their query is incorrect. I’m only one voice, together, we can be two.

    If you really want to use the Health Literacy filter right now… I can offer you a trick. Change all of the quotes from double quotes (“) to single quotes (‘). Then get rid of all of the line breaks (make sure there are only spaces… and that the query wraps). In fact, just use this… it worked for me:

    ‘health literacy’ OR ‘health literate’ OR ‘medical literacy’ OR (health [ti] AND literacy [ti]) OR (functional [tw] AND health [tw] AND literacy [tw]) OR ((low-literate [ti] OR low-literacy[ti] OR literacy[ti] OR illiteracy[ti] OR literate[ti] OR illiterate[ti] OR reading [mh] OR comprehension [mh]) AND (health promotion [major] OR health education [major] OR patient education [major] OR communication barriers [major] OR communication [major:noexp] OR health knowledge, attitudes, practice [major] OR attitude to health[major])) OR (comprehension [major] AND educational status [major])OR (family [ti] AND literacy [ti])OR ((‘drug labeling’ OR Prescriptions [mh]) AND ‘comprehension’) OR ‘adult literacy’ OR ‘limited literacy’ OR ‘patient literacy’ OR ‘patient understanding'[ti] AND english [la]

    Unfortunately, much software depends on a lot of other software (especially internally), so the fix may not be as quickly as you’d hope, but, it will be fixed.

    Additionally, requirements change over time… custom filters are a new requirement, while the “tack” icon is another requirement. They’re not all together compatible right now. We do, however, recognize this, and may try to find a solution in the future.

    Enjoy your filters, and thank twitter’s re-tweets for getting your message across.

    • 2 gossypiboma June 13, 2009 at 3:46 pm

      Hmm, I’ll have to so some more investigating into the single quotation mark thing. I thought they were as anathema at NLM as Canadian spelling.


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