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MEDLIB-L  January 2007, Week 3

MEDLIB-L January 2007, Week 3

Subject:

Re: Quotations and phrase searching in PubMed

From:

"Kwan, Julie" <[log in to unmask]>

Reply-To:

Kwan, Julie

Date:

Wed, 17 Jan 2007 14:41:31 -0800

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (144 lines)

The explanation in PubMed help seems clear -- Go to PubMed Help, search for 'phrase', and then select the link 'Searching for a phrase'. In most cases you shouldn't try to bypass PubMed's Automatic Term Mapping or try to use truncation. Just enter the search terms and check details. Complexity increases when you try to bypass ATM -- and it may limit your retrieval. 

In other words, the most important parts of PubMed Help are the first two sentences -- here's what PubMed Help says:

----

Searching for a phrase

PubMed does not perform adjacency searching. However, many phrases are recognized by the MeSH Translation Table used in PubMed's Automatic Term Mapping (ATM) feature. For example, if you enter fever of unknown origin, PubMed recognizes this phrase as a MeSH concept. If a phrase is not recognized you can instruct PubMed to bypass ATM and search for a phrase using the formats outlined below. 
Examples

    * Enclose the phrase in double quotes: "kidney allograft"
    * Use a search tag: kidney allograft[tw]
    * Use a hyphen: first-line
    * Truncate: kidney allograft*

More information for phrase searching:

    * If you use a hyphen or quotes and the phrase is not found, the hyphen or quotes are ignored and the phrase is processed using automatic term mapping. Phrases may appear in a PubMed record but not be in the phrases index.
    * When you enter your search terms as a phrase PubMed will not perform automatic term mapping that includes explosion of MeSH terms. For example, "health planning" will include citations that are indexed to the MeSH term, Health Planning, but will not include the more specific terms, e.g., Health Care Rationing, Health Care Reform, Health Plan Implementation, etc., that are included with the automatic MeSH mapping.
    * Truncating a word in a multi-word query may result in an unexpected phrase search. For example the search, fetus infection* maternal will treat fetus infection* as a phrase. Check Details to see the search translation.

----

Note: This section is followed by a section on why you should NOT truncate in PubMed unless you really know what you are doing.


Julie Kwan
Library Network Coordinator
NN/LM Pacific Southwest Region
310-825-5342
800-338-7657
[log in to unmask]
http://nnlm.gov/psr

-----Original Message-----
From: Medical Libraries Discussion List [mailto:[log in to unmask]] On Behalf Of Shaffer, Christopher J
Sent: Wednesday, January 17, 2007 7:43 AM
To: [log in to unmask]
Subject: Re: Quotations and phrase searching in PubMed

I've done some additional digging, based on the reply below and suggestions in private email, and I'm still confused.  It appears that, contrary to the explicit statement that PubMed does not perform adjacency searching, it does perform such searching when a phrase is recognized.  Here's an interesting example, using [all fields].

#3 Search "family nursing" [all fields] 640
#2 Search family nursing [all fields] 557
#1 Search family [all fields] AND nursing [all fields] 32471

I'm still confused, but I think I'm confused at a higher level than I was before.  If you run these searches and look at the details, searches #1 and #2 are changed to use MeSH headings, while search #3 is not mapped to any MeSH headings.  Despite my use of the [all fields], that is ignored in searches #1 and #2.  I'm not sure how you would force PubMed to search all fields, since it obviously ignored the search tag in my queries.  Interestingly, PubMed does wildly different mapping of MeSH headings on searches #1 and #2.  It clearly recognizes that family nursing is a phrase in search #2.

I sent the question to the PubMed Help Desk and await a reply.  At many people's request, I will post a summary of responses to the list.

-----
Chris Shaffer, M.S., AHIP, Assistant Director for Technology and Outreach
Hardin Library for the Health Sciences, University of Iowa
319-335-6928 (voice) 319-325-6575 (mobile) 319-353-3752 (fax)
[log in to unmask]   http://www.lib.uiowa.edu/hardin/



> -----Original Message-----
> From: Medical Libraries Discussion List [mailto:MEDLIB-
> [log in to unmask]] On Behalf Of Sieving, Pamela (NIH/OD/ORS) [E]
> Sent: Tuesday, January 16, 2007 8:57 PM
> To: [log in to unmask]
> Subject: Re: Quotations and phrase searching in PubMed
> 
> While I am not much more informed than you are about the inner workings of
> PubMed on phrase searching, one way to examine the differences is to look
> at what cites were retrieved by your second search, within quotes, but not
> retrieved in the first: All of the articles have the phrase in the address
> field.  So the clue here is in the 'all fields' note you saw in the
> details for the second search.
> 
> That disentangles this example, but I hope others will come up with
> additional examples, and some insight into how phrases are sometimes
> disassembled and searched.
> 
> Pam
> 
> Pamela C. Sieving, MA, MS
> Biomedical Librarian/Informationist
> National Institutes of Health Library
> 10 Center Drive  room 1L09G  msc 1150
> Bethesda, Maryland 20892 USA
> 301 451-5862 phone   301 402-0254 fax
> [log in to unmask]
> nihlibrary.nih.gov
> --------
> Amazing Research.  Amazing Help
> 
> 
> -----Original Message-----
> From: Shaffer, Christopher J [mailto:[log in to unmask]]
> Sent: Tuesday, January 16, 2007 4:37 PM
> To: [log in to unmask]
> Subject: Quotations and phrase searching in PubMed
> 
> Has anyone written an easy-to-read, succinct description of how quotations
> and phrase searching work in PubMed?  We'd like something we can use in
> our classes and educational materials.
> 
> Also, does anyone know exactly how it works?  I'm befuddled.  The help
> file seems to have contradictory information.  It explicitly says that
> adjacency searching is not supported.  It further says that quoted phrases
> not found in the MeSH Translation Table are processed using normal
> automatic term mapping.  It goes on to say that quoted phrases will not be
> exploded (does this apply if the phrase is found in the MeSH Translation
> Table? If it is not found?  Both?).
> 
> What happens when a quoted phrase is found in the MeSH Translation Table?
> As far as I can tell, this is not addressed in the help file.
> 
> Why does the following example search return more results for the quoted
> phrase?
> 
> family nursing
>   Details: "family nursing"[MeSH Terms] OR family nursing[Text Word]
>   Results: 556 citations
> 
> "family nursing"
>   DETAILS: "family nursing"[All Fields]
>   Results: 639 citations
> 
> And this search returns more results for the unquoted phrase?
> 
> health planning
>   Details: "health planning"[MeSH Terms] OR health planning[Text Word]
>   Results: 153712 citations
> 
> "health planning"
>   DETAILS: "health planning"[All Fields]
>   Results: 29230 citations
> 
> Here is the URL for the help file.
> 
> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhel
> p.Searching_PubMed#pubmedhelp.Searching_for_a_phra
> 
> -----
> Chris Shaffer, M.S., AHIP, Assistant Director for Technology and Outreach
> Hardin Library for the Health Sciences, University of Iowa
> 319-335-6928 (voice) 319-325-6575 (mobile) 319-353-3752 (fax) chris-
> [log in to unmask]   http://www.lib.uiowa.edu/hardin/

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January 2005, Week 1
December 2004, Week 5
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December 2004, Week 3
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November 2004, Week 5
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April 2004, Week 5
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December 2003, Week 5
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October 2003, Week 5
October 2003, Week 4
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September 2003, Week 5
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September 2003, Week 1
August 2003, Week 5
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June 2003, Week 1
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March 2003, Week 5
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January 2003, Week 5
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December 2002, Week 5
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October 2002, Week 5
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August 2002, Week 5
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July 2002, Week 1
June 2002, Week 5
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March 2002, Week 5
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December 2001, Week 5
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April 2001, Week 3
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April 2001, Week 1
March 2001, Week 5
March 2001, Week 4
March 2001, Week 3
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March 2001, Week 1
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February 2001, Week 1
January 2001, Week 5
January 2001, Week 4
January 2001, Week 3
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January 2001, Week 1
December 2000, Week 5
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December 2000, Week 3
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December 2000, Week 1
November 2000, Week 5
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October 2000, Week 5
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October 2000, Week 3
October 2000, Week 2
October 2000, Week 1
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December 1999, Week 5
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December 1998, Week 5
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December 1998, Week 1
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January 1998, Week 5
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January 1998, Week 3
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December 1997, Week 5
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January 1997, Week 5
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December 1996, Week 5
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January 1996, Week 1
December 1995, Week 5
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December 1995, Week 3
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December 1995, Week 1
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November 1995, Week 3
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October 1995, Week 4
October 1995, Week 3
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December 1994, Week 5
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