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NLM Technical Bulletin

NLM Technical Bulletin 1997 Nov-Dec; 299



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Transitioning from ELHILL to PubMed

[Editor's Note added 1998/03/26: see comment in the NLM Technical Bulletin. 1998 Jan-Feb;(300):e1]

A previous article in the Technical Bulletin (July-August 1997 issue) highlighted the basics of PubMed searching. A listing of some of the PubMed search rules and syntax appears on page 9 in this article. This page may be photocopied or removed to keep for ready reference. PubMed's search rules can be easily used to construct expert search strategies similar to those that users are accustomed to creating using the ELHILL command language. PubMed's search rules are easy to master. Two of the biggest syntax hurdles will be to break the habit of using parentheses rather than square brackets to qualify search terms, e.g., [pt] not (pt), and to remember that Boolean connectors must be entered in uppercase, e.g., AND, OR, and NOT.

PubMed offers certain advantages such as the ability to search against all years of MEDLINE and PREMEDLINE in one fell swoop. And, "Overflow" errors that arise on ELHILL from conditions such as terms that generate a high number of postings or date ranging don't routinely happen on PubMed.

To illustrate how easy it is to convert ELHILL commands into PubMed commands, this article will transform a Technical Bulletin Gold Standard search strategy into a PubMed search strategy. The search "The client is a layperson who wants information on alternative treatments for breast cancer" was taken from the January-February 1997 issue. Figure 1 is the ELHILL search strategy originally formulated for CANCERLIT which explains search statements 9-11.

The PubMed Boolean Search page was used to recreate the ELHILL search strategy, in Figure 1, into a PubMed search. The Boolean Search page is best suited for constructing complex (or lengthy) search strategies--the query box is larger and scrollable which allows you to view your search strategy in full. To get there, click on Advanced Search from PubMed's Homepage and then click on the Boolean Search link.


Figure 1 - ELHILL Search Strategy

SS 1:   exp *breast neoplasms   

SS 2:   exp *alternative medicine

SS 3:   1 and 2

SS 4:   *holistic health or *wit a#d humor or 
	exp *psychotherapy

SS 5:   1 and 4

SS 6:   exp *breast neoplasms/dh

SS 7:   3 or 5 or 6

SS 8:   7 contains eng (la) and 7 contains human (mh) 

SS 9:   8 and 96 (yr) or 8 and 95 (yr) or 8 and 94 (yr) 

SS 10:  8 and 93 (yr) or 8 and 92 (yr) or 8 and 91 (yr)

SS 11:  9 or 10

Before you continue reading, at this point if you are still not familiar with PubMed, it is recommended that you review the listing of PubMed's search rules and syntax on Page 9. Otherwise, the translation detailed below from ELHILL language to PubMed may not be as clear.

The query box on the Boolean Search page must contain the entire search strategy as a single search statement. The first step in converting the ELHILL search strategy into a single search statement for PubMed was to create the three search statements that would be OR'd together (i.e., 3 or 5 or 6). Each of those search statements converted into a PubMed search statement follows:

SS 3: breast neoplasms [majr] AND alternative medicine [majr]

SS 5: holistic health [majr] OR wit and humor [majr] OR psychotherapy [majr] AND breast neoplasms [majr]

SS 6: breast neoplasms/diet therapy [majr]

Note: PubMed automatically explodes MeSH terms, whereas on ELHILL you must specify whether or not a term is to be exploded (e.g., breast neoplasms [majr] is equivalent to exp *breast neoplasms). The ability to turn off an automatic explode will be available soon. So, keep in mind that the same syntax is used for terms that are explodable as well as for terms that do not have any indentions. For example, the MeSH terms, "Holistic Health" and "Wit and Humor" (neither have indentions) are entered as holistic health [majr] and wit and humor [majr] and the explodable MeSH term "Psychotherapy" is entered as psychotherapy [majr].

Boolean search statements are processed left to right. To change the order in which PubMed processes a search statement, enclose the individual concept in parentheses. The terms inside a set of parentheses are processed as a unit and then incorporated into the overall strategy. Below are two examples of how the above PubMed search statements can be OR'd together with or without parentheses:

Example #1:
breast neoplasms [majr] AND alternative medicine [majr] OR (holistic health [majr] OR wit and humor [majr] OR psychotherapy [majr] AND breast neoplasms [majr]) OR breast neoplasms/diet therapy [majr]

Example #2:
alternative medicine [majr] OR holistic health [majr] OR wit and humor [majr] OR psychotherapy [majr] AND breast neoplasms [majr] OR breast neoplasms/diet therapy [majr]

PubMed can handle large explosions for over 9 million citations in a blink of an eye. While you should apply logic in formulating a search, all those lessons about segmenting your terms into separate search statements for computer and cost-efficiency are just not vital to the new PubMed technology. That said, however, PubMed's future plans include a feature where you will be able to view a picture of the strategy--similar to Internet Grateful Med's "Details of Search" button. Here we hope to provide clarifying messages such as terms that have no postings. In addition, the plans also call for this feature to include an edit function so that a search strategy can be easily revised and resubmitted; and intermediate postings shown.

The remaining portion of the search strategy is to apply the search limiters for language (i.e., english), study group (i.e., human), and a date range (i.e., articles published during 1991-1996). Whereas, on ELHILL to apply the desired limits in CANCERLIT took an additional four steps (i.e., ELHILL search statements 8-11), this can be easily translated on PubMed into the syntax below and then added (ANDed) to the search strategy.

english [la] AND human [mh] AND 1991:1996 [dp]

Figure 2 contains the ELHILL Gold Standard search converted into a single PubMed search statement.


Figure 2 - ELHILL search converted to PubMed

alternative medicine [majr] OR holistic health [majr] OR wit and humor [majr] OR psychotherapy [majr] AND breast neoplasms [majr] OR breast neoplasms/diet therapy [majr] AND english [la] AND human [mh] AND 1991:1996 [dp]


To ensure that the ELHILL search strategy was correctly converted to PubMed, the search strategies were run in their respective systems to compare search results. The ELHILL search was run in MEDLINE, MED93, and MED90. In both ELHILL and PubMed, the results were the same -- 37 was the total postings.

If you have any questions or comments about the PubMed search strategy, please contact PubMed customer support by clicking on the "Help Desk" link.

Helpful Hint:

While constructing a complex (or lengthy) search strategy for PubMed, it is helpful to use your word processing software as a scratch pad. Use the word processing software to enter your search terms, the correct syntax (e.g., search field tags enclosed in square brackets, Boolean connectors in all uppercase), and spell check. It helps to use extra spaces or blank lines to separate your concepts for ease of proofreading and checking your logic. Once you are satisfied with the search strategy, "copy and paste" it into the PubMed query box. Be sure to remove all extra spaces, hard carriage returns or other special word processing codes. You can then go back to the search strategy in your word processing software to edit or reformulate the search strategy--quickly and easily. Repeating the "copy and paste" step into the PubMed query box will then let you execute the revised strategy with just a few clicks.

Test Your Skills

Now that you have stepped through the process of translating an ELHILL search strategy into PubMed, why not test your skills? Figure 3 is a rather complex and lengthy ELHILL search strategy for you to translate into PubMed. This example is based on a portion of an ELHILL search used to create the MEDLINE subfile of SPACELINE.

Helpful Hint:

Before you get started, please refer to the Helpful Hint box on page 6 that discusses using your word processing software in conjunction with PubMed for complex and lengthy search strategies.

Once you have completed your translation you can compare it to the PubMed strategy that was constructed by the MEDLARS Management Section as seen in Figures 4 and 5 on page 8.

When the ELHILL search was run against MEDLINE back through MED66 there were 20,997 postings. PubMed yielded 21,107 postings--a difference of 110 postings on the test day. The tested ELHILL search differed from the strategy in Figure 3 in only one way--the first two MeSH terms were exploded in order to compare the total postings to PubMed because the automatic explosion of MeSH in PubMed cannot be turned off yet. Even with that adjustment PubMed had higher postings, though. Why the difference you ask? Remember, PubMed is a single database that not only includes all of MEDLINE (1966 to present) but PREMEDLINE as well. In addition, there are citations, labeled as [Record as supplied by publisher], which are electronically-supplied to NLM by the publisher. These citations are first received by PubMed before being processed into PREMEDLINE and eventually MEDLINE. In addition, for those electronically supplied citations, from journals that are selectively indexed (e.g. Science or Nature), the non-indexed citations remain in PubMed even though they never become MEDLINE citations. The additional 110 citations found by PubMed for this search were confirmed to be either PREMEDLINE or publisher supplied citations.

Conclusion

In both the Gold Standard search and the Test Your Skills search you can see how a complex and lengthy ELHILL strategy can be transitioned to PubMed with equivalent results. Learning any new system is a challenge. As we work together with your direct feedback on your needs as information providers, PubMed will keep evolving to make it easier and clearer as evidenced by the future plans for the "Details of Search button."

--prepared by Carolyn Tilley, Lou Knecht and Rhonda Allard
MEDLARS Management Section

Figure 3 -Test Your Skills. Convert this ELHILL Search Strategy into PubMed

SS 1:   space flight or extraterrestrial environment  or 
	aerospace medicine  or submarine medicine or cosmic 
	radiation

SS 2:   (ad) ames and research  and center

SS 3:   2 and not iowa (ad) and not ia (ad) and not all 
	agricult: (ad)

SS 4:   (ad) johnson and space and center or kennedy and 
	space and center or goddard  and space and center or 
	marshall and space and center or stennis and space 
	and center

SS 5:   (ad)  national and aeronautics and space or nasa 

SS 6:   5 and not spain (ad) and not france (ad)

SS 7:   (tw) space and agency

SS 8:   (tw) canadian or european or all japan: or  french or 
	german

SS 9:   7 and 8

SS 10:  (tw) centre and national and etudes and spatiales

SS 11:  (tw) deutsche and agentur and raumfahrtangelegenheiten

SS 12:  blomqvist cg or booth f or booth fw or buckey jc or 
	cintron nm or convertino v or convertino va or 
	czeisler ca or daunton ng or dillaman rm or dudley ga 
	or fitts rh or fortney s or fortney sm or fox ge or 
	ganong wf or genant hk or hargens ar or hockstein li 
	or horrigan dj jr or ingber de or jee ws or jukes th

SS 13:  kanavarioti a or keil lc or koch kl or kretsinger rh 
	or lacey jc jr or lackner rd or lambertsen cj or 
	lanyi jk or leach cs or loeppky ja or malacinski gm 
	or margulis l or mcfeters ga or meehan rt or 
	moore-ede mc or morey er or morey-holton e or 
	morey-holton er or musacchia xj

SS 14:  orgel le or pak cy or partridge nc or perachio aa or 
	pierson dl or ponnamperuma c or reschke mf or ross md 
	or rumbaugh dm or schneider vs or schor rh or 
	tipton cm or tischler me or vandenburgh hh or 
	vailas ac or waligora jm or west jb or whalen rt or 
	wilt f or wilt fh or woese cr or wolgemuth dj

SS 15:  (jc) kxc or ppj or bp5 or 2rq or 9ja or bx7 or ok7 
	or ok8 or ux6

SS 16:  1 or 3 or 4 or 6 or 9 or 10 or 11 or 12 or 13 or 
	14 or 15

Figure 4 - Test Your Skills ELHILL Search Converted to PubMed as it Might Appear in a Word Processing Document

space flight [mh] OR extraterrestrial environment [mh] OR aerospace medicine [mh] OR submarine medicine [mh] OR cosmic radiation [mh] OR

(ames [ad] AND research [ad] AND center [ad] NOT (iowa [ad] OR ia [ad] OR agricult* [ad])) OR

((johnson [ad] OR kennedy [ad] OR goddard [ad] OR marshall [ad] OR stennis [ad]) AND space [ad] AND center [ad]) OR

((national [ad] AND aeronautics [ad] AND space [ad] OR nasa [ad]) NOT (spain [ad] OR france [ad])) OR

(space [tw] AND agency [tw] AND (canadian [tw] OR european [tw] OR japan* [tw] OR french [tw] OR german [tw])) OR

(centre [tw] AND national [tw] AND etudes [tw] AND spatiales [tw]) OR

(deutsche [tw] AND agentur [tw] AND raumfahrtangelegenheiten [tw]) OR

blomqvist cg OR booth f OR booth fw OR buckey jc OR cintron nm OR convertino v OR convertino va OR czeisler ca OR daunton ng OR dillaman rm OR dudley ga OR fitts rh OR fortney s OR fortney sm OR fox ge OR ganong wf OR genant hk OR hargens ar OR hockstein li OR horrigan dj jr OR ingber de OR jee ws OR jukes th OR

kanavarioti a OR keil lc OR koch kl OR kretsinger rh OR lacey jc jr OR lackner rd OR lambertsen cj OR lanyi jk OR leach cs OR loeppky ja OR malacinski gm OR margulis l OR mcfeters ga OR meehan rt OR moore-ede mc OR morey er OR morey-holton e OR morey-holton er OR musacchia xj OR

orgel le OR pak cy OR partridge nc OR perachio aa OR pierson dl OR ponnamperuma c OR reschke mf OR ross md OR rumbaugh dm OR schneider vs OR schor rh OR tipton cm OR tischler me OR vandenburgh hh OR vailas ac OR waligora jm OR west jb OR whalen rt OR wilt f OR wilt fh OR woese cr OR wolgemuth dj OR

kosm biol aviakosm med [ta] OR probl kosm biol [ta] OR adv space biol med [ta] OR aviakosm ekolog med [ta] OR aerosp med [ta] OR aviat space environ med [ta] OR orig life [ta] OR orig life evol biosph [ta] OR space life sci [ta]


Figure 5 - Test Your Skills ELHILL Search Converted to Pubmed as it Should Appear in the PubMed Query Box

space flight [mh] OR extraterrestrial environment [mh] OR aerospace medicine [mh] OR submarine medicine [mh] OR cosmic radiation [mh] OR (ames [ad] AND research [ad] AND center [ad] NOT (iowa [ad] OR ia [ad] OR agricult* [ad])) OR ((johnson [ad] OR kennedy [ad] OR goddard [ad] OR marshall [ad] OR stennis [ad]) AND space [ad] AND center [ad]) OR ((national [ad] AND aeronautics [ad] AND space [ad] OR nasa [ad]) NOT (spain [ad] OR france [ad])) OR (space [tw] AND agency [tw] AND (canadian [tw] OR european [tw] OR japan* [tw] OR french [tw] OR german [tw])) OR (centre [tw] AND national [tw] AND etudes [tw] AND spatiales [tw]) OR (deutsche [tw] AND agentur [tw] AND raumfahrtangelegenheiten [tw]) OR blomqvist cg OR booth f OR booth fw OR buckey jc OR cintron nm OR convertino v OR convertino va OR czeisler ca OR daunton ng OR dillaman rm OR dudley ga OR fitts rh OR fortney s OR fortney sm OR fox ge OR ganong wf OR genant hk OR hargens ar OR hockstein li OR horrigan dj jr OR ingber de OR jee ws OR jukes th OR kanavarioti a OR keil lc OR koch kl OR kretsinger rh OR lacey jc jr OR lackner rd OR lambertsen cj OR lanyi jk OR leach cs OR loeppky ja OR malacinski gm OR margulis l OR mcfeters ga OR meehan rt OR moore-ede mc OR morey er OR morey-holton e OR morey-holton er OR musacchia xj OR orgel le OR pak cy OR partridge nc OR perachio aa OR pierson dl OR ponnamperuma c OR reschke mf OR ross md OR rumbaugh dm OR schneider vs OR schor rh OR tipton cm OR tischler me OR vandenburgh hh OR vailas ac OR waligora jm OR west jb OR whalen rt OR wilt f OR wilt fh OR woese cr OR wolgemuth dj OR kosm biol aviakosm med [ta] OR probl kosm biol [ta] OR adv space biol med [ta] OR aviakosm ekolog med [ta] OR aerosp med [ta] OR aviat space environ med [ta] OR orig life [ta] OR orig life evol biosph [ta] OR space life sci [ta]


Notes:

Author Searching: Currently, PubMed searches an author name having an initial or initials the same way ELHILL does. With the next system update, the search rules for author searching will change to incorporate automatic truncation that can be turned off. This will affect how this search would be translated to PubMed in the future.

Be advised that unqualified author names can retrieve from other fields such as the abstract where references may be cited.

Journal Titles: In Figure 3, the 3-character journal code (e.g., 2rq (jc)) was used to retrieve citations to specific journals on ELHILL. In PubMed, the 3-character journal code is not searchable. Instead, you can use the MEDLINE title abbreviation (e.g., aerosp med [ta]) or the full title (e.g., aerospace medicine [ta]) to retrieve citations from specific journals.


PubMed Search Rules and Syntax

Boolean Syntax:

  1. Boolean operators, AND, OR, NOT must be entered in UPPERCASE. Please note that the ELHILL connector "and not" is simply the single word NOT on PubMed.

    Because PubMed only recognizes Boolean operators in uppercase, it is no longer necessary to use a symbol to disguise MeSH terms that contain Boolean operators. For example, the MeSH term Wit and Humor must be entered in ELHILL as wit a#d humor using the hash mark to "hide" the word and. But in PubMed you simply enter wit and humor [mh].

  2. PubMed processes all Boolean connectors in a left-to-right sequence. You can change the order in which PubMed processes a search statement by enclosing an individual concept in parentheses. The terms inside the set of parentheses will be processed as a unit and then incorporated into the overall strategy. On ELHILL, all AND statements are processed first.

  3. When you enter a Boolean search statement, PubMed will automatically parse the search terms on either side of the Boolean operator into a single phrase. For example, cigarette smoking AND therapy will only search for cigarette smoking as a phrase, not cigarette AND smoking AND therapy.

    In addition, if PubMed finds a phrase within a search strategy string that uses unqualified terms it will automatically search the terms as a phrase rather than simply combining them. For example, if you enter air bladder fistula in the PubMed query box, PubMed will search "air bladder" as a phrase. If you do not want this automatic phrase parsing enter each term separated by the Boolean operator AND, e.g., air AND bladder AND fistula.

Truncation:

  1. To truncate a term, use an asterisk (*) at the end of a search term. For example, bacter* will retrieve bacteria, bacterium, bacteriophage, etc. OR'd together automatically. Whereas on ELHILL, in addition to using the colon truncation symbol, you have to use the instruction word "all" to avoid getting an ELHILL Multi-Meaning message (e.g., all bacter:).

    Note: There is no single-character truncation symbol such as the pound sign (#) used on ELHILL.

Date and Date Range Format:

  1. Dates or date ranges must be entered using the format YYYY/MM/DD [dp], e.g. 1997/10/06 [dp] . The month and day are optional (e.g., 1997 [dp] or 1997/03 [dp]). To enter a date range, insert a colon (:) between each date (e.g., 1993:1995 [dp] or 1997/01:1997/06 [dp]).

    Note: To specify a publication date or range, it is recommended that you search only by year (e.g., 1996 [dp] or 1995:1997 [dp]). Journals vary in the way the publication date appears. Some journals include just the year, whereas others include the year plus month or year plus month plus day. And, some journals use the year and season (e.g.,Winter 1997). The publication date is recorded as it appears in the journal.

Search Field Qualification:

Terms can be qualified using PubMed's search field tags. Note: A list of search field tags is available in PubMed's online help under Search Fields.

  1. Terms must be post-qualified, such as aromatherapy [mh] not [mh] aromatherapy.

  2. Search field tags must be enclosed in brackets, e.g., [mh] not (mh).

  3. Case does not matter nor does spacing, e.g., crabs [mh] = Crabs[mh].

  4. Terms that are qualified with the Text Words field tag [tw] will be searched for in the Title, Abstract, MeSH headings and Subheadings, and Names of Substance. Whereas, on ELHILL Subheadings are not included in a Text Word search. Some additional fields will be added to PubMed's [tw] soon.

MeSH Terms, Subheadings, and Language

MeSH Terms:

  1. MeSH Terms must be qualified using the search field tags, e.g., [mh] for MeSH Terms or [majr] for Major MeSH Topic. The asterisk (*) which on ELHILL is used for MeSH Major Topic is reserved for truncation in PubMed.

  2. MeSH terms are automatically exploded to include the more specific terms. The ability to turn off this automatic explosion is coming soon to PubMed.

    Note: Searching with MeSH terms will exclude PREMEDLINE citations as they have not yet been indexed with MeSH.

Subheadings:

  1. You can directly attach subheadings using the format MeSH Term/subheading (spelled out), e.g., neoplasms/diet therapy [majr]. The ability to use the two-letter subheading abbreviations will be available soon. In addition, only one subheading may be directly attached to a MeSH term, e.g., neoplasms/diet therapy [majr] OR neoplasms/drug therapy [majr]

  2. The Subheading field and search field tag (e.g., [sh]) will be available soon in PubMed so that multiple Subheadings can be "free-floated" in a search strategy.

Language:

  1. Language must be spelled out. The 3-character abbreviation search (e.g., eng) is coming soon to PubMed.

    Note: The ELHILL expression "and not for (la)" was devised to aid in computer efficiency. Negating about 25% of MEDLINE citations (those that are foreign language) is much more efficient and less costly than limiting to 75% of MEDLINE (those that are English) on ELHILL. This shortcut is not necessary on PubMed. So, you can now use the syntax AND english [la] on PubMed without worrying about overloading the system.

Rev. 1/98

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