*4. Constructing a comprehensive keyword search for a drug class or for a non-drug concept

Objectives:

The student will:

1. Understand and be able to explain the steps involved in creating a keyword search strategy
2. Know which terms should be included in a search for articles about a specific drug or class of drugs and know where these terms can be located
3. Be able to list the types of alternate terms that should be included in a search statement for a non-drug concept and know how to find such terms.
4. Be able to use truncation, quotation marks, Boolean operators, and parentheses correctly in a keyword search.
5. Know how to use messages above the PubMed search result list and information in the “History and Details” table to revise a search.
6. Know which filters can be used without eliminating retrieval of unindexed records and how to limit a search to unindexed records.
7. Know how to document a search.

Reminder: Objective 1.  Understand and be able to explain the steps involved in creating a keyword search strategy

An outline of the steps in the keyword searching process is shown in the box below.  We will go through each of these steps.

Reminder of Step 1 — Outline search concepts

As you will remember, the first step in a performing a keyword search is listing the search concepts.  When you completed the tasks assigned in the previous chapter, you listed the important search concepts in two searches, the “demonstration” search and the “final search assignment” search.    Review that work now (see below).

What are the major concepts in the “Demonstration” search?

• demonstration topic = Does the available evidence support the use of omacetaxine in CML?

What are the major concepts in the “final search assignment” search?

• final search assignment topic = Does the available evidence support the efficacy of nilotinib in treatment of BCR-ABL+, chronic myeloid leukemia that is resistant to one of the other anti-cancer drugs?

Reminder –  Objective 2a.   Know which terms should be included in a search for articles about a specific drug  and know where these terms can be located

I’ve demonstrated construction of a search for articles about omacetaxine, you’ve composed a search for articles about nilotinib.

Reminder –  Objective 2b.   Know which terms should be included in a search for articles about a  class of drugs and know where these terms can be located

In this chapter and in part I of this week’s assignment ( a search for articles about nasogastric administration of proton pump inhibitors), you will briefly consider the terms needed in a search for an entire drug class.   For the exam, you should know which terms are included in a “drug class” search strategy.

Objective 3.  Be able to list the types of alternate terms that should be included in a search statement for a non-drug concept and know how to find such terms.

Most searches include a non-drug concept.  Our “demonstration” search topic includes the “chronic myelogenous leukemia” concept.   Your “final search assignment” search topic, also includes the “chronic myelogenous leukemia (CML)” concept.  In addition,  your “final search assignment” topic includes a “resistance” concept.

This week, as you complete the FSA 2 assignment, you will:

• find the terms needed for the “resistance” concept,
• create a search strategy for that concept, and then
• join the “resistance” strategy with the “CML” strategy created during this week’s demonstration, and the “nilotinib” strategy you created last week.

Designing a search for the CML concept

I recommend that you work through the steps yourself as you watch me demonstrate the process of designing a keyword search for the “Chronic Myelogenous Leukemia” search.  The text below also describes these steps.

Optional video demonstrating construction of the “CML” search The video shows  the steps described in the text below.  It includes construction of the CML search strategy, combining that strategy with the omacetaxine search strategy, and production of the various forms of the search needed for the final search assignment.

Gathering synonyms or relevant terms from the discussion/assignment that stimulated the search.

If you have been observing carefully, you will notice that I’ve used a couple different terms for the CML concept in this Pressbook.

• CML
• chronic myeloid leukemia
• chronic myelogenous leukemia

I would begin the process of creating a search strategy by listing these in Word.

Always keep track of the different words that your fellow students, colleagues, teachers, or preceptors use when they describe a research project or search topic

Other synonyms that are known to you ⭐

Based on my knowledge of the topic, I could add several synonyms to the list we’ve derived.  Do you know of any synonyms?  It’s unlikely that you do at this stage in your career.

Using the MeSH database to find alternate keywords ⭐

Next, I recommend that you use the MeSH database to look for new synonyms and related terms.

A warning: 

The MeSH database was actually created to help searchers find the exact heading for their concept and add this heading to a MeSH (medical subject heading) search.   During today’s tasks, we will not be using the MeSH database for the purpose for which it was created.  Do NOT use the “Add to Search Builder” button this week!

Go to the MeSH database

• Start by navigating to the PubMed website.

Two routes to the UNMC version of PubMed are available to you.

Either:

• • Click the “Library” link in Canvas and then click the MEDLINE via PubMed link.

or

• • Go to the Library’s homepage http://www.unmc.edu/library, click  on the “Resources” menu, then the “Literature Databases” link,  and finally the “PubMed” link/button.
• Next, click on the “MeSH Database” link under the “Explore” icon on the right-hand side of the PubMed homepage.

Search for the concept of interest

• Enter your concept (in this case — chronic myeloid leukemia ) in the search box and click the “Search” button or hit the “Enter/Return” key on your keyboard.

• If more than one heading is offered, click on the relevant heading.  If more than one heading is relevant, start with the first relevant heading, and, later, repeat the steps in the next section for the second relevant heading, and so on.

In this case, there are two headings for chronic myeloid leukemia.  Remember that the final search assignment question is focused on the typical, bcr-abl-positive CML.

Scan the heading definition for new search terms

Scan the heading definition.  Are any new terms for your search concept present in the definition?   Our list already includes:

• CML
• chronic myeloid leukemia
• chronic myelogenous leukemia

In this case, there is a term for chronic myelogenous leukemia in the heading itself:

• leukemia, myelogenous, chronic, BCR-ABL Positive

We’re creating a keyword search to search the title and abstract.  We need words and phrases in speaking/writing order Our search is not intended as a method for searching indexes.  The heading shown in the bullet point above is in indexing order (it contains commas).    Don’t include the phrases that containing commas in your keyword searches for this class . Convert any indexing-order terms harvested from the MeSH database into writing/speaking order. The speaking/writing order for this heading phrase is:

• BCR-ABL Positive chronic myelogenous leukemia

Let’s add this term to our term list.

• CML
• chronic myeloid leukemia
• chronic myelogenous leukemia
• BCR-ABL Positive chronic myelogenous leukemia.

Does the definition under the heading contain any new terms that should be added to our list?

Words like “pluripotent stem cells”, “myeloid cells”, and “bone marrow” are frequently used in discussions of CML, but are not specific to discussions of CML.  In other words,  these terms could equally be present when normal bone marrow or other bone marrow diseases are being discussed.

The various CML phases (“chronic phase”, “accelerated phase”, and “blast crisis”) are mentioned in the definition.  I can tell you that it would be very unusual to mention one of these terms in a title or abstract pertaining to CML without also mentioning one of the names for CML.  The general CML terms will, thus, find the articles about phases of CML.  The phase names do not need to be included in the CML concept.

Review the entry terms

The entry term list is a list of terms for which the heading is used.  If you ‘entered’ any of these terms in a MeSH database search box and hit your keyboard’s “Return” button,  you would end up with the heading you’re currently viewing.

Here’s the list of  entry terms for the “Leumkemia, myelogenous, chronic, BCR-ABL positive” heading.  The entry terms in indexing order that are also represented in this list in speaking/writing order are highlighted.  They will be removed.

• Leukemia, Chronic Myelogenous
• Leukemia, Chronic Myeloid
• Leukemia, Granulocytic, Chronic
• Leukemia, Myelocytic, Chronic
• Leukemia, Myelogenous, Chronic
• Leukemia, Myelogenous, Ph1 Positive
• Leukemia, Myelogenous, Ph1-Positive
• Leukemia, Myeloid, Chronic
• Leukemia, Myeloid, Ph1 Positive
• Leukemia, Myeloid, Ph1-Positive
• Leukemia, Myeloid, Philadelphia Positive
• Leukemia, Myeloid, Philadelphia-Positive
• Myelocytic Leukemia, Chronic
• Chronic Myelocytic Leukemia
• Chronic Myelocytic Leukemias
• Leukemia, Chronic Myelocytic
• Leukemias, Chronic Myelocytic
• Myelocytic Leukemias, Chronic
• Myelogenous Leukemia, Chronic
• Chronic Myelogenous Leukemia
• Chronic Myelogenous Leukemias
• Leukemias, Chronic Myelogenous
• Myelogenous Leukemias, Chronic
• Myelogenous Leukemia, Ph1-Positive
• Leukemia, Ph1-Positive Myelogenous
• Leukemias, Ph1-Positive Myelogenous
• Myelogenous Leukemia, Ph1 Positive
• Myelogenous Leukemias, Ph1-Positive
• Ph1-Positive Myelogenous Leukemia
• Ph1-Positive Myelogenous Leukemias
• Myeloid Leukemia, Chronic
• Chronic Myeloid Leukemia
• Chronic Myeloid Leukemias
• Leukemias, Chronic Myeloid
• Myeloid Leukemias, Chronic
• Myeloid Leukemia, Ph1-Positive
• Leukemia, Ph1-Positive Myeloid
• Leukemias, Ph1-Positive Myeloid
• Myeloid Leukemia, Ph1 Positive
• Myeloid Leukemias, Ph1-Positive
• Ph1-Positive Myeloid Leukemia
• Ph1-Positive Myeloid Leukemias
• Myeloid Leukemia, Philadelphia-Positive
• Leukemia, Philadelphia-Positive Myeloid
• Leukemias, Philadelphia-Positive Myeloid
• Myeloid Leukemia, Philadelphia Positive
• Myeloid Leukemias, Philadelphia-Positive
• Philadelphia-Positive Myeloid Leukemia
• Philadelphia-Positive Myeloid Leukemias
• Granulocytic Leukemia, Chronic
• Chronic Granulocytic Leukemia
• Chronic Granulocytic Leukemias
• Granulocytic Leukemias, Chronic
• Leukemia, Chronic Granulocytic
• Leukemias, Chronic Granulocytic

I  removed the highlighted indexing-order terms (all of which were already present in writing/speaking order in the entry term list) from the list, combined the remaining (unhighlighted) terms with my previously assembled list of names for CML, and removed the duplicates.

This is a long list of phrases and soon we will have to add a British version of leukemia (leukaemia).  This will nearly double the length of the phrase list.     Also, one can imagine other variants (e.g. BCR-ABL positive granulocytic leukemia).   In this case, it’s possible to make the search shorter (and more exhaustive) by breaking the concept into subconcepts.

Have you noticed that most of the names for CML contain at least three words and these three words represent different subconcepts that are part of the chronic myeloid leukemia concept: subconcept 1 – leukemia, subconcept 2 – myeloid, subconcept 3 – other term indicating chronic nature ?

• CML
• chronic myeloid leukemia
• chronic myelogenous leukemia
• BCR-ABL Positive chronic myelogenous leukemia.

• Chronic Myelocytic Leukemia
• Chronic Myelocytic Leukemias
• Chronic Myelogenous Leukemias
• Ph1-Positive Myelogenous Leukemia
• Ph1-Positive Myelogenous Leukemias
• Chronic Myeloid Leukemias
• Ph1-Positive Myeloid Leukemia
• Ph1-Positive Myeloid Leukemias
• Philadelphia-Positive Myeloid Leukemia
• Philadelphia-Positive Myeloid Leukemias
• Chronic Granulocytic Leukemia
• Chronic Granulocytic Leukemias

Rather than trying to represent all of the possible phrases, its easier to make a three subconcept term — ((leukemia terms) AND (myeloid terms) AND (chronic terms)) — that will be OR’d with the abbreviation CML (which contains all three subconcepts in one word).  I find it easiest to represent subconcepts in columns of a table.   The table below contains a  column for each of the three sub-concepts.  A record that has one term from column 1, one term from column 2 and one term from column 3 will probably be about chronic myeloid leukemia.  The CML term represents all 3 sub-concept columns in a single term.

CML

Review any  “Previous Indexing” and “See Also” headings.

Not all headings have “Previous indexing” or “see Also” headings, but some do.  In the MeSH database record, scroll down to look at the area immediately below the “Entry Term” list.  This is where “Previous Indexing” and/or “See Also” entries will appear if they are present.

The “Leukemia, Myelogenous, Chronic, BCR-ABL Positive” record in the MeSH database has a “Previous Indexing” section.  Both of the headings shown are too broad for our search.  If they were relevant, we would, after reviewing narrower headings, click on each of the “Previous Indexing”  headings and look at their definitions, entry terms, previous indexing/see also sections, and narrower headings to try to gather additional terms for our search.

The “leukemia, myelogenous, chronic, BCR-ABL positive” record in the MeSH database doesn’t have a “See also” section.  Below, I’ve inserted an image of the “See Also” section in the MeSH record for “Alcoholism.”

If our the MeSH database record for our “leukemia, myelogenous, chronic, BCR-ABL positive” heading had a “See Also” section, we would, after reviewing narrower headings, click on each of the relevant “See Also”  headings and look at their definitions, entry terms, previous indexing/see also sections, and narrower headings to try to gather additional terms for our search.

Narrower headings

The final area of the MeSH database record to review is the MeSH tree area at the bottom of the page.  Sometimes the narrower headings need to be included as alternate terms for a search concept.  If so, the records for these narrower headings should also be accessed.  The heading definitions, “Entry Term” lists, “See Also” lists, “Previous Indexing” lists, and narrower headings of the narrower headings are possible sources of additional search terms..

The narrower headings for the “Leukemia, Myelogenous, Chronic, BCR-ABL Positive” heading are just the phases of CML.  As mentioned earlier, when writers discuss these phases of CML, they always mention CML(or a CML synonym).   The phase names are not stand-alone terms for CML. Consequently, you don’t have to include terms for the phases in your CML search strategy.

We’ve now completed gathering terms from the relevant MeSH database records and have the following.

CML

Other  sources:  relevant article/s, internet search, suggestions from others

You will have a chance to look at other sources for alternate keywords during coming assignments and exercises.

• Reading relevant article/s (this week’s lab)
• Internet search (Lab correction session)
• Suggestions from others (Lab correction session)

Additional terms found during those assignments and exercises will be included in your final search assignment.

• Exhaustive searching is usually a cyclical process  —  After the searcher performs a search, they gather additional search terms, revise their search strategies, run the revised searches.  When reviewing results of the revised searches, they sometimes find new search terms and, thus, must revise again, search again, etc.
• Exhaustive searching is a group process.  Exhaustive searching typically begins with individual work on a search strategy, but  consultation with others is required ( per guidelines for writing systematic reviews) and often results in addition of new search terms or reworking of a search strategy.    When working on an exhaustive search for a systematic review, I am expected to solicit feedback from one or more other searchers and expected to rework my search strategies based on any valid feedback and suggestions received.    I will require that you rework your final search assignment searches based on feedback from others (including feedback from me).   I want you to understand that this part of the process is required of professional searchers as well of student searchers.

Consider tips for making your search more exhaustive

After gathering a list of terms for your concept, consider the following tips for making your search more exhaustive.  The text below the box covers these tips one at a time.

1. Eliminate unecessary words and 2. Add [tiab] to terms that might be present in irrelevant fields

In this search, the “positive” portion of  BCR-ABL-positive, Ph1-positive, and Philadelphia-positive is  unnecessary.   BCR-ABL, Ph1, and Philadelphia will retrieve any records containing the longer phrases that include -positive.

What if an author uses a “+” rather than -positive?   A PubMed search for — BCR-ABL — will retrieve articles containing either — BCR-ABL —  or — BCR-ABL-positive — or — BCR-ABL+.    I could not guarantee that a search for —  BCR-ABL — in UNMC’s other literature databases would retrieve records containing — BCR-ABL+ .  If you’re composing a keyword search for use in several different databases, you might be best served by adding a wildcard (an asterisk) to your search terms as in —  BCR-ABL*.

When you want to find a place name like “Philadelphia” or “hospital” or “medical center” in a title or abstract, but do not want to find all the records that contain these words in the authors’ addresses, add the [tiab] (title abstract) tag to the end of the term.  As in —

Philadephia*[tiab]

CML

Importance for other searches:

Another important example of removing unnecessary words, is seen when one searches for articles about eponymous diseases.   “Eponymous” diseases are conditions that are named after people (usually the physician that first described the condition in the scientific literature or occasionally the  first described patient).  An example is —

Parkinson’s disease

It’s best to remove the word “disease” , truncate the eponym, and add a [tiab] tag.  A PubMed search for —

Parkinson*[tiab]

— will find PubMed records containing any of the following in title or abstract —

• Parkson’s Disease
• Parkinson Disease
• Parkinsons Disease
• Parkinsonian symptoms
• Parkinson’s Syndrome
• etc.

–,  but will not retrieve records solely because one of the authors’ last names is Parkinson.

2.  Think about synonyms again after gathering a list of terms.

After you’ve gathered a list of alternate terms, it’s worth spending a moment or two asking yourself about any additional synonyms.

Occasionally, when authors discuss chronic neoplasms, they call them smoldering or slow-growing.

CML

3.  Include British and American spellings

Leukemia has a British spelling (leukaemia) as does smoldering (smouldering).

CML

I don’t expect you to know which terms have British spellings.⭐   If I mention in a test question that a term has a British spelling and provide that spelling, be sure to check to make sure the search strategy includes that spelling.

4.  Include plurals and singulars (or truncate to allow retrieval of both)

The only noun in our CML search (leukemia) is already present in singular and plural forms.

5.  Include alternate verb forms (or truncate to allow retrieval of all )

The adjective smouldering could also be a verb

CML

6.  Include noun forms of verbs, adjectives, adverbs and vice versa (or truncate to allow retrieval of both)

CML

7.  Include opposites

By “include opposites”.  I mean think about how your concept might be expressed with an opposite term.  In our search, the chronic concept might be non-acute.  This is a bit of a stretch .  However, other concepts do have likely relevant opposites.  For example, tooth whiteners, might be discussed as preparations that remove tooth staining.

CML

8. Include hyphenated and non-hyphenated, space-free versions of words when these exist.

There are several hyphenated terms which might (even if grammatically incorrect) be present without hyphens.  Non-acute might be spelled as nonacute

CML

9. Include spelled-out versions and standard abbreviations for your terms

The 9th tip for making searches exhaustive is to include both spelled-out versions of terms and standard abbreviations.    This does not mean you have to include spelled-out phrases, rather you must either: 1) include spelled-out phrases or 2) terms that will retrieve the spelled-out phrases.  We are taking the second approach to spelled-out terms.  We have one abbreviation already.   It is very hard for first-year pharmacy students to know which abbreviations are standard and which are abbreviations have only been use by an author to simplify writing of an article.    I can tell you that a second standard abbreviation for CML is CGL.  If you search the internet (e.g. Google) for–

medical acronym CGL

— you will find that this abbreviation/acronym is used for chronic granulocytic leukemia.

Objective 4.  Be able to use truncation, quotation marks, Boolean operators, and parentheses correctly in a keyword search.⭐

Next we will apply truncation, quotation marks, Boolean operators, and parentheses.  I like to group my terms before I start this stage.  The grouping may be alphabetical or may simply put like terms together — so the hyphenated and non-hyphenated forms of a particular phrase/term are together.  For example:

CML, CGL

Truncation

Appropriate truncation shortens your search strategy and helps you retrieve relevant word forms you might not have considered.   Newly truncated terms in the table below are in red-font.  The presence of these truncated terms eliminates the need for all the yellow-highlighted terms.

You may wander why I haven’t used — leuk*.  This is because — Leuk* — in addition to retrieving records containing the words — leukemia, leukaemia, leukemias, leukaemias, leukemic and leukaemic — would retrieve records containing — leukocytes, leukophoresis, leukopenia, leukodystrophy, leukotomy, etc.    Truncating after a single syllable often causes this type of problem.    Another example of a problematic truncated single-syllable search term,  is — cat* .  Cat* retrieves articles about pet cats, but  also retrieves records containing — catalysis, catastrophe, catenation, cataplexy, etc.

CML, CGL

Quotes

Quotes must now be added around any multi-word, space-containing  phrases.  Alternatively, the spaces in a multi-word phrase may be replaced by hyphens since PubMed and the other databases licensed by UNMC will take a search for a hyphenated phrase like — slow-growing —  and find records containing either the hyphenated form  (slow-growing) or a space containing form (slow growing).

CML, CGL

Parentheses, Boolean operators ⭐

The box below contains an overview of the steps that follow:

Here’s the process step-by-step:

OR alternate terms for subconcepts

Alternate terms for a subconcept must be OR’d first.

CML, CGL

Place Parentheses () around subconcepts

Parentheses must be added to enclose the OR’d together terms for the subconcepts.

CML, CGL

Join disparate subconcepts with AND

ANDs must be used to join the disparate subconcepts.

(BCR-ABL* OR chronic* OR non-acute OR nonacute OR Ph1* OR Philadelphia*[tiab] OR slow-growing OR smolder* OR smoulder*)  AND  (granulocyt* OR myelo*) AND (leukaem* OR leukem*)

CML, CGL

Place parentheses () around the multi-subconcept term.

To ensure that the multi-subconcept term is treated like a term equivalent to the other terms in the concept, it must be placed inside parentheses.  This ensures that the ANDs inside the multi-subconcept term are performed before the OR’s that will join the multi-subconcept term to the other terms in the concept.

((BCR-ABL* OR chronic* OR non-acute OR nonacute OR Ph1* OR Philadelphia*[tiab] OR slow-growing OR smolder* OR smoulder*)  AND  (granulocyt* OR myelo*) AND (leukaem* OR leukem*))

CML, CGL

Join the multi-subconcept term with other terms for the concept with OR

(( BCR-ABL* OR chronic* OR non-acute OR nonacute OR Ph1* OR Philadelphia*[tiab] OR slow-growing OR smolder* OR smoulder*)  AND  (granulocyt* OR myelo*) AND (leukaem* OR leukem*)) OR CML OR  CGL

Place parentheses () around  all terms for the concept

In preparation for joining the CML concept with the omacetaxine (our other search concept).  We must place parentheses around all the terms for the CML concept.

(((BCR-ABL* OR chronic* OR non-acute OR nonacute OR Ph1* OR Philadelphia*[tiab] OR slow-growing OR smolder* OR smoulder*)  AND  (granulocyt* OR myelo*) AND (leukaem* OR leukem*)) OR CML OR  CGL)

You should use this strategy for the CML concept in your “final search assignment” search.  Remember, exhaustive searching is a group process.  It includes your own work, but also includes suggestions and even whole strategies created by others or that you create with a group.  Professional searchers use searches created by other too (see my search blog for examples of searches created by myself and others and then shared)

Join disparate concepts with AND

Now it’s time to join the two concepts (the “omacetaxine” concept and the “CML” concept) in this “demonstration” search  with AND.

(((BCR-ABL* OR chronic* OR non-acute OR nonacute OR Ph1* OR Philadelphia*[tiab] OR  slow-growing OR smolder* OR smoulder*)  AND  (granulocyt* OR myelo*) AND (leukaem* OR leukem*)) OR CML OR  CGL) AND (Omacetaxin* OR 26833-87-4 OR Ceflatonin OR CGX-635 OR CGX635  OR Homoharringtonine OR NSC-141633 OR NSC141633 OR Chuan-Shan-Ning OR Fu-Er OR Gao-Rui-Te OR Hua-Pu-Le OR Jin-Nuo-Xing OR Sai-Lan OR Wo-Ting OR Synribo)

The following drug names were omitted from the keyword search statement because they were used frequently to indicate discussion of irrelevant concepts and were causing retrieval of irrelevant results:  HHT

When you work on your FSA search,  be sure you carry your lists of removed terms into the documentation for your complete keyword search .

Objective 5.  Know how to use messages above the PubMed search result list and information in the “History and Details” table to revise a search. ⭐

Now it’s time to copy the search strategy, paste it into PubMed, and run the search.

Look at the messages above the search result list

After the “omacetaxine AND CML” search is run, several messages appear above the search result list (see screenshot below).

Make any needed revisions in your search strategy, enter the new strategy in the search box and run the search.

After you run the revised search, look at the area above the search results again.  Is the “asterisk” message still present?

Look at the “Details”

Look at the “Details” for  the revised search.

• Check the information at the top of the “Query” column to be sure the revision you just made in the search strategy appears there.
• Look at the “Translations” section (at the bottom of the “Details” section.
  • Are any of the terms in the ‘Translations” section irrelevant?

Return to the results page and scan the highlighted or bold-faced terms

The purpose of these next steps is to see if relevant results are being retrieved.

• To return to the search results, find the row for your revised search in the “History and Details” table.  Click on the number in the “Results” column.

• Look above your result list and to the right.  What is the current “Sorted by” order?
• If you’re currently looking at the results in “Best Match” order, click the “Display Options” button, click the “Sort by” choice to open the drop-down and select the “most recent” option.

When you’re troubleshooting a search strategy, you don’t want to look at the best results first; you want to see those that fit the criteria less precisely.

• Look for the highlighted or bold-faced terms in the results.
  • The majority of bold-faced or highlighted terms should indicate a discussion of one of the search concepts.  (Highlighted numbers are an exception.  Ignore highlighted numbers if another highlighted term is present that is used in a manner relevant to your search topic).
  • All the results should contain both a CML-related term/s and a omacetaxine-related term.

In the screenshot below, the 8th and 9th results (as of 8/2/2022)  both appear to be irrelevant.  However, #8 does contain both a “CML” concept term and an “omacetaxine” concept term in the “Summary” view.    #9’s summary view contains neither a full CML term nor an omacetaxine term.  If one clicks on the title of #9, one finds that a term for the omacetaxine concept is present (homoharringtonine).  However, I can’t find a term for the “chronic” subconcept of the three subconcept CML term.  If you find the “chronic” term, please, let me know!   If one continues to look through the first 20 or so results, one finds that all others contain terms representing the omacetaxine and CML concepts and the majority are actually relevant.  Remember, most well-constructed, exhaustive keyword searches will retrieve some irrelevant results.    

Troubleshooting will be covered in more detail in the tutorial that guides your assignment and in the assignment correction chapter.

Objective 6.  Know which filters can be used without eliminating retrieval of unindexed records and how to limit a search to unindexed records ⭐

One reason to perform a keyword search is to insure that unindexed records  will be retrieved.  It’s important to be cautious when applying filters when you are trying to retrieve unindexed records.

Know which filters can be used without eliminating retrieval of unindexed records

The filters are shown on the left-hand side of the page.

When you reach PubMed through the Library’s webpage a set of filters selected by the Library appears at the top of the filter column.

The “systematic rev + meta-analyses + guidelines” filter, one of the filters that allows retrieval of unindexed as well as indexed results is among these filters.  Well-done systematic reviews and meta-analyses are at the top of the evidence pyramid ( the highest level of evidence available).⭐  Practice guidelines are sometimes based on systematic reviews but are sometimes based on expert opinion.

“Publication date” filters are immediately available in the filters column.  Remember, you can apply a “publication date” filter without eliminating retrieval of unindexed records.  However, there is rarely a reason to apply a “publication date” filter to an exhaustive search.

The “language” filters are the last of the filters that can be applied without eliminating retrieval of unindexed records.  These are not immediately available in the filters column.

• To see the “language” filters, click on the “Additional Filters” button.

• In the pop-up box that appears, click on the “Language” option, check the “English” option,  and then click the “Show” button.

• The “English” filter will appear in the “Filters” column.
• Click on the box in front of “English” to apply the filter.

Know how to limit a search to unindexed records

For reasons that will be discussed again during the chapter concerning MeSH searching, it is best to search PubMed with both MeSH and keyword searches.  If you are searching the indexed part of PubMed (MEDLINE) with the subject headings (MeSH) added by indexers,  you may want to limit your keyword search to retrieval of unindexed records (records that can not be retrieved by your MeSH search).

The method for limiting a search to unindexed records has been mentioned previously in this course.

Objective 7.  Know how to document a search.

To document a search with filters, it is best to copy the search as it appears on the “Advanced” page in the “History and Search Details” table.  To document the search just performed, I would:

• Click on the “Advanced” link.

• Scroll down to the “History and Search Details” table.

• You may select and copy the entire relevant row (selection of the entire row is shown in the screenshot below) and paste it into a Word document.

• You may select and copy just the essential portion of the “Query” column (see screenshot below) and paste it into a Word document.  Be sure to include all parentheses and the Filters you selected.  The word “Search:” at the beginning of the information in the column and the “Sort by” order are not essential.

• After documenting the actual search strategy and filters, be sure to also record the terms you removed from the search strategy.    Documentation for the search might look as shown below:

(((BCR-ABL* OR chronic* OR non-acute OR nonacute OR ph1 OR ph1+ OR Philadelphia*[tiab] OR slow-growing OR smolder* OR smoulder*) AND (granulocyt* OR myelo*) AND (leukaem* OR leukem*)) OR CML OR CGL) AND (Omacetaxin* OR 26833-87-4 OR Ceflatonin OR CGX-635 OR CGX635 OR Homoharringtonine OR NSC-141633 OR NSC141633 OR Chuan-Shan-Ning OR Fu-Er OR Gao-Rui-Te OR Hua-Pu-Le OR Jin-Nuo-Xing OR Sai-Lan OR Wo-Ting OR Synribo) Filters: English

The following drug names were omitted from the keyword search statement because they were used frequently to indicate discussion of irrelevant concepts and were causing retrieval of irrelevant results:  HHT

• If you have added UNMC’s  “systematic rev + meta-analyses + guidelines”  filter, it will not be shown in the “History and Search Details” table.   You would need to copy and paste the information already described and then add a note under the search strategy similar to that shown in the highlighted row below:

(((BCR-ABL* OR chronic* OR non-acute OR nonacute OR ph1 OR ph1+ OR Philadelphia*[tiab] OR slow-growing OR smolder* OR smoulder*) AND (granulocyt* OR myelo*) AND (leukaem* OR leukem*)) OR CML OR CGL) AND (Omacetaxin* OR 26833-87-4 OR Ceflatonin OR CGX-635 OR CGX635 OR Homoharringtonine OR NSC-141633 OR NSC141633 OR Chuan-Shan-Ning OR Fu-Er OR Gao-Rui-Te OR Hua-Pu-Le OR Jin-Nuo-Xing OR Sai-Lan OR Wo-Ting OR Synribo) Filters: English

“systematic rev + meta-analyses + guidelines”  filter applied –> 1 result

The following drug names were omitted from the keyword search statement because they were used frequently to indicate discussion of irrelevant concepts and were causing retrieval of irrelevant results:  HHT

Assignment

Note:  When submitting search strategies in your assignments for this class.  DO NOT submit the “Search Details” that are shown when the “Details” column arrow is facing downward!  Submit the search strategy that is still present when the “Details” arrow is pointing to the right.

You will complete two searches with the guidance of online tutorials.

•  The first search is a search for articles about nasogastric administration of proton pump inhibitors.  It is guided by the a tutorial entitled “Advanced Keyword Searching, Part I“.  The assignment is outlined in the tutorial and is submitted through Canvas.
• The second search is a search for articles about your final search assignment topic “efficacy of nilotinib in BCR-ABL+ CML that is resistant to another anti-cancer drug” .  This part of the assignment is outlined in the tutorial entitled “Advanced Keyword Searching, Part II.”  It is submitted through Canvas as the FSA2 assignment.
  • You should use the corrected version of your nilotinib search strategy (including corrections made based on my (Cindy’s) comments in the Canvas grade center)
  • You should use the CML search strategy created in this chapter for the CML concept:

(((BCR-ABL* OR chronic* OR non-acute OR nonacute OR ph1 OR ph1+ OR Philadelphia*[tiab] OR slow-growing OR smolder* OR smoulder*) AND (granulocyt* OR myelo*) AND (leukaem* OR leukem*)) OR CML OR CGL)

• • The tutorial will help you create a list of terms for the “resistance” concept and then join this to the nilotinib and CML strategies.

• Cindy will mark your initial work as pass/fail (adequate or inadequate).
• After the submission deadline for this assignment, you will go through the troubleshooting chapter and video and then correct your own work.  You are encouraged to consult classmates.  You  will submit the search with your corrections as your “FSA 2 corrected” assignment. Cindy will provide detailed comments on your corrected work.

Questions, Problems, Text Errors?

Before you leave, …

• Do you have any questions or do you feel that clarification of some aspect of the materials would be helpful?
• Have you noticed any errors or problems with course materials that you’d like to report?
• Do you have any other comments?

If so, you can submit questions, comments, corrections, and concerns anonymously — or with your e-mail (your choice) — through this online form .  Alternatively, you’re always welcome to contact Cindy Schmidt directly 402-650-5056, cmschmidt@unmc.edu, or by making an appointment to meet with Cindy via Zoom.

Answers to questions or requests for clarification that are submitted anonymously will be answered in Canvas on the “Discussions” page for this course.