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.

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5 responses

25 09 2008
PubReMiner; a nice PubMed ‘added-value’ tool « (the) health informaticist

[...] endoscopy, anti-ulcer agents, gastritis, peptic ulcer” etc. It’s nice. I like it. Laika will tell you all about it in much more detail. [...]

8 03 2009
Advanced Neuritis in PubMed « Laika’s MedLibLog

[...] Although you can look up MeSH assigned to each individual citation in PubMed in the citation display… [...]

30 06 2009
10 + 1 PubMed Tips for Residents (and their Instructors) « Laika’s MedLibLog

[...] 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. [...]

5 11 2009
Consejos de PubMed para residentes « Biblioteca Virtual Ribera

[...] 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. [...]

8 12 2011
fraiz

RT@ LibrarianGMIT: New useful search engine that returns full PDF scientific articles not subject to access fees: http://www.freefullpdf.com

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