How to construct searches using either a user defined group of fields or the database specific ‘multi-purpose’ (.mp) set of fields as provided by Ovid.

Background

When using the Advanced Search mode in a bibliographic database like Ovid MEDLINE, it is common practice to enter a search term followed by the field or fields you want Ovid to search in. For example, the search expression (adolescent$ or young adult$).ti,ab,kf. (see this Focused Search, line #1) tells Ovid to search for the terms adolescent or adolescents or young adult or young adults in the Title (TI) field as well as the Abstract (AB) and Keyword Heading (KF) fields. This kind of search is referred to as a qualified search in the sense that the instruction to the database is explicit, namely “go and look for these specific terms in these specific fields, that I, the user have selected.”

But as noted in a previous Focused Search, databases vary not only in size but also in terms of their “shape”. You may, for instance, be uncertain about the field composition or layout of the database. In such cases Ovid can help out with the multi-purpose or .mp search. This is described as an unqualified search across a default set of fields which are specific to the database being used.

In this case, the example as used above would be entered as (adolescent$ or young adult$).mp. For Ovid MEDLINE the default set of fields across which Ovid will then search are:

title, book title, abstract, original title, name of substance word, subject heading word, floating sub-heading word, keyword heading word, organism supplementary concept word, protocol supplementary concept word, rare disease supplementary concept word, unique identifier, synonyms, population supplementary concept word, anatomy supplementary concept word.

By contrast, for Embase the default set of fields across which Ovid will search are:

title, abstract, heading word, drug trade name, original title, device manufacturer, drug manufacturer, device trade name, keyword heading word, floating subheading word, candidate term word.

Because the default fields to be covered by an .mp search are pre-determined, .mp based searches lend themselves well to cross database searching. In this sense the .mp search option is a helpful supplement to Ovid’s Basic Search which is also able to carry search expressions easily across multiple databases.

Practice Suggestions:

1. Combine and compare this Focused Search with the Basic Search example, Knowledge Discovery with NLP (Basic Search) – All Databases. Note that in the Basic Search the search line adolescents adhd ritalin adverse effects {Including Related Terms} has as its search type Basic. But when you limit this line to Five Stars, the search type changes to Advanced. This now enables you to combine this result set with the results in this .mp example. Do the numbers differ greatly?
2. Use the Change option to run this Focused Search through Embase on Ovid. Do both versions of the search, i.e. the lines using .ti,ab,kf. as opposed to .mp, run properly? How could you easily compare the results obtained in Ovid MEDLINE with those from Embase on Ovid?
3. Use the Change option to run this Focused Search through APA PsycInfo. Do both versions of the search, i.e. the lines using .ti,ab,kf. as opposed to .mp, run properly? How can you tell? Identify two markers that tell you.

Strategy

(adolescent$ or young adult$).ti,ab,kf. [Version 1: User defined group of fields]

(adhd or Attention Deficit Hyperactivity Disorder).ti,ab,kf.

(ritalin or methylphenidate$).ti,ab,kf.

(adverse effect$ or adverse event$ or untoward effect$).ti,ab,kf.

1 and 2 and 3 and 4

(adolescent$ or young adult$).mp. [Version 2: Ovid .mp defined group of fields]

(adhd or Attention Deficit Hyperactivity Disorder).mp.

(ritalin or methylphenidate$).mp.

(adverse effect$ or adverse event$ or untoward effect$).mp.

6 and 7 and 8 and 9

How to fine tune individual search lines as well as whole search queries using user-selected criteria, called ‘limits’.

Background

When constructing a search question it is helpful to separate out the search terms and phrases from additional criteria that can be used to systematically reduce your database results down to a manageable number of references. Such additional criteria could be the type of publication; a journal article, a review, a specific type of review, e.g. Cochrane or ACP, a case report or even a letter or  editorial. Other additional criteria could include narrowing down the result set by language or by time. In the context of searching for information on databases, imposing such additional criteria upon a search is referred to as applying ‘limits’. Whilst the idea of employing limits is common to A&I databases, the variety and scope of the ‘limits’ options available to searchers can differ between databases.    

This Focused Search introduces an initial selection of limits available for Ovid MEDLINE. These are displayed in the image below.

The limits can be selected and applied sequentially (see lines #6,#7 and #8) or imposed in a single step (see line #9). The full range of limits available for the database you are searching in, can be viewed and selected by clicking on the Additional Limits option at the bottom of the initial selection display. You can also place the limits, most useful to you, on the initial selection display by selecting the Edit Limits option. Your selection will remain as your initial display selection for the duration of your database session. After which they will return to and re-display the default selection.

For database administrators, please note  however, that the default selection can be customized for you by Ovid Technical Support so that the default selection of limits better addresses your users’ needs. 

Practice Suggestions

1. From the results shown in line #5, how many of them are from preprint servers?
2. Line #6 removes from the total number of records, those that do not have abstracts. Use the NOT operator to determine how many of these records there are? Could they nevertheless still be relevant to the search query? How could you assess this?
3. Name four of the common structural elements seen in records with structured abstracts. Tip: Display the records involved using Ovid’s Complete Reference display option.

Strategy

(adolescent$ or young adult$).mp. [Version 2: Ovid .mp defined group of fields]

(adhd or Attention Deficit Hyperactivity Disorder).mp.

(ritalin or methylphenidate$).mp.

(adverse effect$ or adverse event$ or untoward effect$).mp.

1 and 2 and 3 and 4

limit 5 to abstracts

limit 6 to full text

limit 7 to yr=”2020 -Current”

limit 5 to (abstracts and full text and yr=”2020 -Current”)

An introduction to the system and structure of the controlled vocabulary, based upon medical subject headings, that lies behind the bibliographic database Ovid MEDLINE.

Background

Drawing again on the idea of the ‘size and shape’ of databases, this Focused Search provides an introduction to the structure and system of the MeSH thesaurus. The MeSH thesaurus is a controlled vocabulary, based upon medical subject headings. It has been created and is maintained by the National Library of Medicine (NLM) in the USA. The MeSH thesaurus is a domain specific knowledge base curated by humans, that aids both document classification as well as discoverability and retrieval.

MeSH Structure and System

Ovid MEDLINE is Ovid’s rendering of the PubMed database, it too created and maintained by NLM. The content of this kind of bibliographic database consists, for the most part, of records of documents that have been indexed using a controlled vocabulary. A controlled vocabulary is a hierarchical term classification system where terms, representing a thing or concept, can be located within the controlled vocabulary system, along with its broader and narrower terms. For an informative optical rendering of this enter the search term ‘migraine disorders’ into the MeSH database search box as shown below.

https://www.ncbi.nlm.nih.gov/mesh/?term=migraine+disorders

The returned screen provides detailed background information on the target term. Amid the detail is also an indication of where the target term, here ‘migraine disorders’ appears in the MeSH term hierarchy. In the enhanced diagram below the blue bordered terms represent the broader terms associated with ‘migraine disorders’. By contrast the thinner green bordered expressions are its narrower terms. Which is to say that the idea or concept represented by the MeSH term ‘migraine disorders’ can itself be further broken down into finer ideas or sub-concepts, specifically ‘Alice in Wonderland Syndrome’, ‘Migraine with Aura’, ‘Migraine without Aura’ and ‘Ophthalmoplegic Migraine’.

Understanding the MeSH term constellation for your target terms or terms, and being able to navigate through the thesaurus hierarchy effectively, will greatly assist you in the systematic construction of high quality search queries.

In PubMed the MeSH database is a stand-alone, albeit connected, knowledge resource. By contrast the MeSH thesaurus is fully integrated into the Ovid MEDLINE search experience. MeSH terms can be easily located in the thesaurus hierarchy and narrower terms selected (as well as deselected) either as a group or individually as you decide. When you choose to include all of the MeSH terms narrower terms, you are said to have “exploded” the term. The Explode function and a related function, called Focus will be covered in the next Focused Search, Knowledge Discovery with MeSH (Explode & Focus) – Ovid MEDLINE.

Practice Suggestions:

1. Go to the Advanced Search. Check that the option Map term to Subject Heading is activated, that is ticked, and enter as a Keyword the expression migraine disorders. Looking at the screen that is subsequently displayed, list at least 4 options you could act on from there.
2. Go again to the Advanced Search. Deselect the option Map term to Subject Heading and as before enter as a Keyword the expression migraine disorders. Looking at the screen that is subsequently displayed, what kind of search has Ovid executed? Where do you think Ovid has searched for your term?  
3. In the Focused Search used in this example, how can you verify that the results in line #2 are included in the .mp search, run in line #3?

Strategy

migraine disorders.ti.

migraine disorders.ti,ab.

migraine disorders.mp.

Migraine Disorders/

exp Migraine Disorders/             

exp Migraine Disorders/ or migraine disorders.mp.

How to instruct the database to include narrower terms in a MeSH thesaurus search and/or to retrieve only those terms considered main subject terms.

Background

This Focused Search provides further background on the structure and system of the MeSH thesaurus. The MeSH thesaurus is a controlled vocabulary, based upon medical subject headings. It has been created and is maintained by the National Library of Medicine (NLM) in the USA. The MeSH thesaurus is a domain specific knowledge base curated by humans, that aids both document classification as well as discoverability and retrieval.

MeSH Structure and System
Ovid MEDLINE is Ovid’s rendering of the PubMed database, it too created and maintained by NLM. The content of this kind of bibliographic database consists, for the most part, of records of documents that have been indexed using a controlled vocabulary. A controlled vocabulary is a hierarchical term classification system where terms, representing a thing or concept, can be located within the controlled vocabulary system, along with its broader and narrower terms. Broader terms are those for which your chosen term is a narrower term or sub-concept. Narrower terms on the other hand are the narrower terms or sub-concepts of your chosen term.

Using MeSH for Targeted Searching
We have already seen how, on Ovid, you can use the Advanced Search search mode to locate a term in a specific field (i.e. migraine.ti., see line #1 in this Focused Search) or in a group of fields (i.e. migraine.mp., see line #2).

In the Advanced Search, with mapping turned on (which for most users is a default setting) you can search for a thing not just in terms of the characters that describe it i.e. ‘migraine’, but also in a conceptual sense. That is you are able to automatically include additional terms and phrases that more fully represent the concept that best describes the thing you are looking for. In this Focused Search the entry term for all 10 search lines, using the Advanced Search with mapping turned on, is migraine. With mapping turned on, our search journey starts and continues through the MeSH thesaurus where at various stages we are offered opportunities to expand upon or narrow the scope of our search (see lines #3 to #10).

To investigate this further, let’s consider the following research question and subsequent task.

Is acupuncture effective in the treatment of migraines? Find randomised controlled trials.

From the research question, let us describe the population group as ‘migraine sufferers’ and that by proceeding with the search term ‘migraine’ we are likely to capture a relatively high proportion of relevant documents.

Upon entering the term migraine into the Advanced Search search mode with mapping turned on, Ovid maps our entered term onto a MeSH term, in this case Migraine Disorders/ (see line #3).  Clicking on the MeSH terms displays it in the context of its occurrence and positioning within the controlled vocabulary  as displayed below. Here we can see that Migraine Disorders is a sub-term of the broader term, Headache Disorders, Primary. But Migraine Disorders is itself the broader term for its narrower terms, namely Alice in Wonderland Syndrome, Migraine with Aura, Migraine without Aura and Ophthalmoplegic Migraine.

The returned display, which highlights the mapped to term Migraine Disorders/, also tells us that a specific number of documents, indicated by the search results have been indexed with that specific term. In other words, the concept or idea represented by the term ‘migraine’ within a constellation of scope defining broader and narrower terms, has been identified in the database. This, as opposed to ‘just’ occurrences of the word ‘migraine’ as is the case in lines #1 and #2.

Explode and Focus Options
The MeSH thesaurus, both in terms of its structure and direct integration in Ovid MEDLINE, also facilitates systematic searching. The scope of a selected MeSH term can be expanded upon by selecting the Explode option next to the selected term. See the green highlighting in the screen shot above. MeSH terms displayed in a search strategy with the ‘exp’, as shown in line #5 of the displayed Focused Search, tells us that the total number of records returned for that search line includes the MeSH term along with its narrower terms. By contrast, selecting the Focus option, highlighted in purple above, reduces the scope of the term, whether exploded or not, to records where the selected MeSH term represents one of the main topics as described in the article. The ‘*’ character placed before the MeSH term, as displayed in line #4 , indicates that the search has been run with this more specific requirement in mind. 

MeSH Subheadings
Each MeSH term has a collection of subheadings associated with it. The list of subheadings for the MeSH term Migraine Disorders is displayed in the screen shot below.

As part of MeSH thesaurus construction and maintenance, the indexers at NLM allocate subheadings to MeSH terms. Subheadings provide an additional means of further fine-tuning the context within which the MeSH term, i.e. the concept, is being sought. In the displayed Focused Search, lines #6, #7 and #8 return records that cover Migraine Disorders but specifically those related to the etiology, diagnosis and prevention and control of the condition respectively. It is also possible to select multiple subheadings as shown with respect to therapy, in line #9. 

Practice Suggestions

1. Does the subheading /dh – Diet Therapy include vitamin or mineral supplements? Use the ‘i’ icon next to the subheading to find out.   
2. How many PubMed-not-MEDLINE records would you expect to find in line #5 of the displayed Focused Search? Look at the Focused Search, Database Size and Shape (docz.dz) – Ovid MEDLINE to help you find the answer.
3. Describe what Ovid is doing in line #10 of the displayed Focused Search. In terms of database record status, what type or types of database record are being returned with this search? Would this search also run in Embase on Ovid although it has been formulated using MeSH terms?

Strategy

migraine.ti.

migraine.mp.

Migraine Disorders/

*Migraine Disorders/

exp Migraine Disorders/             

exp Migraine Disorders/et [Etiology]

exp Migraine Disorders/di [Diagnosis]

exp Migraine Disorders/pc [Prevention & Control]

exp Migraine Disorders/dh, dt, th [Diet Therapy, Drug Therapy, Therapy]           

exp Migraine Disorders/ or migraine.mp.

How to use the controlled vocabulary in Ovid MEDLINE to contrast terms, assess their coverage, relevance to the research question and then select them accordingly.

Background

The structure, system and sheer depth of database controlled vocabularies also provides searchers with various means of selecting terms, of considering their relevance and of refining them so that they better suit the search at hand. To illustrate this, let us refer again to the following research question and subsequent task.

Is acupuncture effective in the treatment of migraines? Find randomised controlled trials.

Here we need to consider how to proceed with the term ‘acupuncture’. This Focused Search looks at how the MeSH thesaurus as an highly structured and contextually deep knowledge base can help researchers refine their search terms. And that via Ovid MEDLINE, the MeSH thesaurus knowledge base provides researchers with a means of being able to (a). navigate through it, (b). select specific terms and (c). deselect others.   

Exact versus Near Matches
Entered into the Advanced Search with the mapping turned on, the entry term acupuncture yields a list of MeSH term possibilities as shown in the screen shot below. As marked by the ticked Select box, the entry term acupuncture is an exact match. The other possibilities are near matches.

From this initial display, or by running the MesH term search in Ovid MEDLINE (line #1), it is not possible to determine whether or not Acupuncture/ has narrower terms. Running the term again but with the Explode option activated, indicates that it does not (#2).  However, Acupuncture Therapy/ does have narrower terms (compare lines #3 and #4), terms that might be more appropriate for the research question. 

Learning with Scope Notes
The MeSH thesaurus created and cultivated by the NLM is an exceptionally information laden example of a controlled vocabulary. In addition to a hierarchical term classification scheme, rich structure and subheadings, MeSH terms also have scope notes allocated to them. This MeSH term specific annotation gives an indication of the coverage of the term (from the indexers point of view), flags points to note, provides information on the year of entry of the MeSH term into the thesaurus, indicates any previous indexing, gives references and lists other terms the given MeSH term would additionally capture when used in a search. In this Focused Search example the scope note for Acupuncture Therapy/ helpfully draws a distinction between the term ‘acupuncture’ meaning the specialty as opposed to ‘acupuncture’, a form of therapy. See lines #6 and #7. 

Targeted Term Selection
In contrast to the MeSH term Acupuncture/ which has no narrower terms, Acupuncture Therapy/ has several. However, not all of them might be pertinent to the research question at hand. In Ovid MEDLINE it is possible to fully display the chosen MeSH term and all its narrower terms and their narrower terms, yet only select specific narrower terms. In the screen shot example below the Acupuncture Therapy/ narrower terms Electroacupuncture and Moxibustion as highlighted in red, have been excluded.

Practice Suggestions:

1. How many narrower terms are there for the MeSH term “Drug-Related Side Effects and Adverse Reactions”/?
2. How could you verify that Explode returns narrower terms as well as the narrower term of the narrower terms?
3. Would the MeSH term Deep Learning/ usefully contribute to an investigation on surface versus deep learning in medical education? How could you find out?

Strategy

Acupuncture/

exp Acupuncture/

Acupuncture Therapy/

exp Acupuncture Therapy/

acupuncture therapy/ or acupuncture analgesia/ or acupuncture, ear/ or meridians/ or acupuncture points/

Acupuncture/ [A sub-category of "Health Occupations"]

Acupuncture Therapy/ [A sub-category of "Complementary Therapies"]

How to use the MeSH thesaurus’s scope notes to build up lists of free term search expressions associated with your MeSH terms.

Background

A major strength of abstracting and indexing (A&I) databases, such as Ovid MEDLINE and Embase on Ovid, is that their enormous content is indexed against a controlled vocabulary or thesaurus. As discussed in previous Focused Searches, these knowledge resources are used to systematically organize, classify and give structure to the database’s content.

However, not all records can be captured using thesaurus based searches. To remedy this situation it is good practice to search on concepts, not only expressed by their equivalent thesaurus term description,  but also using free terms. A ‘free term’ is a word or phrase that describes the thing you are searching for but is not dependent on being part of a controlled vocabulary. A free term search has the additional benefit that we can search for terms across all the database fields that make up the database record.

The question then arises how do we determine which free term words and phrases would be appropriate to use? We can of course simply add them ourselves, drawing them from our own knowledge of the subject matter. Another approach is to avail of the list of terms a thesaurus indicates that its thesaurus term covers. In Ovid MEDLINE, and more specifically the MeSH thesaurus, this information can be found in the respective MeSH term’s Scope Note as indicated below.

Clicking upon the ‘i’ icon displays the full entry for the MeSH term. The scope note describes, as the expression implies, the extent or scope of meaning associated with the term, additional notes on the term, the year of entry of the MeSH term into the thesaurus and a list of Used For terms.

These ‘Used For’ terms, as displayed in the screen shot below, are a list of term variations, singular or plural forms, alternative spellings and synonyms that the indexer watches for in the indexable medical literature. Then, due to their conceptual parity the indexer makes and marks the direct connection between these terms as used in the literature and the term in the thesaurus that, in effect, represents them. So for example, where an article talks of ‘sick headaches’ or ‘status migrainosus’ these articles will be captured by the thesaurus search Migraine Disorders/ but not necessarily by migraine*.ti,ab. or migraine*.mp.    

The purpose of this Focused Search is twofold. Firstly, to flag scope notes as a source representing a comprehensive list of free terms that due to their close semantic connection to their associated thesaurus terms can help you supplement your thesaurus based searches. Secondly, to demonstrate that it is not necessary to try and render all the ‘Used For’ terms into a free term search expression. Particularly in the case of MeSH, closer examination shows that many such used for terms are entered twice, i.e. firstly in full and then as an inverted version. And that with truncation the overall number of term variants can be reduced. The screen shot below presents an example of how all the 35 Used For terms for Migraine Disorders/ can be condensed and rendered  into a search expression as minimalist as (migraine$ or sick headache$ or status migrainosus).mp.

Book an Ovid Coaching session for this Focused Search to learn how to systematically convert the Used For Terms for both for the MeSH term Migraine Disorders/ and its exploded equivalent exp Migraine Disorders/ using a five step process so as to be able to construct the comprehensive concept searches as indicated in lines #1 to #3 and #4 to #6 respectively.

Step 1. Prepare the List of Used For Terms
Step 2. Remove the Inversions
Step 3. Truncate the Terms
Step 4. Construct the Search Expression
Step 5. Save the Search Expression in Line Format (Optional)

Practice Suggestions

1. At the MeSH term mapping screen, in addition to selecting MeSH terms and their exploded versions, you can additionally also select an .mp. rendered version of your search term. Do this for the entry term ‘migraines’. How close is the number of these results compared to the detailed search strategy discussed in the Focus Search?
2. In the Focused Search example the term ‘migraine’ is truncated as ‘migraine$’ to capture singular and plural forms of the word. Are there any advantages to truncating the term as ‘migrain$’? How could you determine this?
3. The two search expressions (alice in wonderland syndrome).mp. and (alice adj2 wonderland syndrome).mp yield the same number of results. Are there any advantages to using the ADJn operator?

Strategy

Migraine Disorders/

(abdominal migraine$ or acute confusional migraine$ or cervical migraine syndrome$ or migraine variant$ or migraine$ or sick headache$ or status migrainosus).mp.

1 or 2

exp Migraine Disorders/             

(abdominal migraine$ or acute confusional migraine$ or cervical migraine syndrome$ or migraine variant$ or migraine$ or sick headache$ or status migrainosus or alice in wonderland syndrome or acute onset aura migraine or basilar artery migraine or basilar migraine$ or basilar type migraine or classic migraine or classical migraine or complicated migraine or familial hemiplegic migraine$ or hemiplegic-ophthalmoplegic migraine or migraine aura without headache or migraine with acute onset aura or migraine with aura$ or migraine with prolonged aura or migraine with typical aura or prolonged aura migraine or typical aura without headache or common migraine$ or migraine without aura or ophthalmoplegic migraine syndrome$ or ophthalmoplegic migraine$).mp.

4 or 5