How to incorporate a search filter from an external, third-party source into your own Ovid search libraries and documents (Part 1).

Background

One of the main drivers behind the OvidGO! / Focused Searches project is to make searches, and especially search filters, discoverable, actionable and useable. Search filters, searches designed to achieve a specific outcome, are particularly challenging. On the one hand they are spread across a large variety of publication vehicles, e.g. journal articles, systematic reviews, websites etc.. A consequence being that many of them are “locked” in analogue formats, most notably print. On the other hand, the role and value of search strategies, filters or otherwise, as the informational foundation of systematic reviews is understated. And as a result, problematic.

An analysis of critically assessed systematic reviews using the KSR Evidence database (also available on Ovid), demonstrates – dramatically – that a large number of currently available systematic reviews have to be marked as having a high risk of bias because they have not at all, or only partially, reported on the search strategies employed for their construction. Ovid’s search strategy construction and sharing functionality, used purposefully and systematically, can help remedy this situation.  

Taking as its reference the Adverse Events (AE) filter published by the European Medicines Agency (EMA), this Focused Search provides an example of what is meant by making search filters, discoverable, actionable and useable.

As part of its pharmacovigilance obligations and activities the EMA is mandated to keep a watching brief over some 300 substance groups and 100 herbal substance groups. Specifically, to monitor medical literature and enter relevant information into the EudraVigilance database. This the EMA does by running search strategies on EMBASE (Embase.com) that combine (a). a comprehensive list of terms describing the target drug or herbal substances, together with (b). an extensive list of terms and phrases that refer to adverse events in a variety of ways. The list of substances and the AE filter used is available from the EMA and is published and updated regularly. A link to the published document is given below.

The current version of the AE filter, displayed below, can be found on page 13.

AND ('adverse drug reaction'/exp OR adverse:de,ab,ti OR 'side effect':de,ab,ti OR 'side effects':de,ab,ti OR 'side effect':lnk OR 'drug overdose'/exp OR overdos*:de,ab,ti OR 'drug misuse'/exp OR misus*:de,ab,ti OR 'drug abuse'/exp OR 'substance abuse'/exp OR abus*:de,ab,ti OR 'pregnancy'/exp OR pregnan*:de,ab,ti OR 'pregnancy complications'/exp OR 'lactation'/exp OR 'breast feeding'/exp OR ('milk human'/exp AND 'secretion'/exp) OR 'fertility'/exp OR 'reproduction'/exp OR 'fetus'/exp OR 'embryo'/exp OR terat*:de,ab,ti OR 'drug efficacy'/exp OR 'drug withdrawal'/exp OR 'medication error'/exp OR 'death'/exp OR death*:de,ab,ti OR fatal*:de,ab,ti OR 'drug interactions'/exp OR 'drug interaction'/exp OR 'carcinogenicity'/exp OR carcinogen*:de,ab,ti OR mutagen*:de,ab,ti OR 'off label drug use'/exp OR 'occupational exposure'/exp OR 'toxicity'/exp OR toxic*:de,ab,ti OR pharmacotox*:de,ab,ti OR neurotox*:de,ab,ti OR cardiotox*:de,ab,ti OR nephrotox*:de,ab,ti OR immunotox*:de,ab,ti OR hepatotox*:de,ab,ti OR cytotox*:de,ab,ti OR immunocytotox*:de,ab,ti OR 'intoxication'/exp OR 'congenital disorder'/exp OR 'drug treatment failure'/exp OR 'case report'/exp OR 'case reports':de,ab,ti OR 'environmental exposure'/exp OR 'treatment contraindication'/exp OR 'drug contraindication'/exp OR 'injury'/exp OR suicide:de,ab,ti OR 'poisoning'/exp OR 'drug tolerance'/exp/mj OR 'treatment failure'/exp/mj OR 'drug resistance'/exp/mj OR 'substance-related disorders'/exp OR 'treatment failure'/exp OR 'drug resistance'/exp OR 'drug resistance':lnk) AND [humans]/lim

So that you can also use this search filter on Ovid, we have translated the Embase.com syntax into Embase on Ovid syntax. Availing of the ABC format options behind Focused Searches, you can display the Ovid rendered version by clicking on ACTIONS / Display. Alternatively, ACTIONS / Launch will run the filter in Embase on Ovid. If you would like to talk to a member of the Ovid Training Team about the filter, select ACTIONS / Ovid Coaching. Once in the database you can combine the filter with substances relevant to your investigation. You can also save the filter in My Workspace for re-use as part of your own or institutional library of searches and search blocks. 

The next Focused Search, Search Blocks in Line Format (EMA AE Filter) – Embase (Part 2), will consider the relative merits of this filter in its paragraph format vis-à-vis a line-by-line format.  

Strategy

exp adverse drug reaction/ OR adverse.hw,ab,ti. OR side effect.hw,ab,ti. OR side effects.hw,ab,ti. OR side effect.fs. OR exp drug overdose/ OR overdos*.hw,ab,ti. OR exp drug misuse/ OR misus*.hw,ab,ti. OR exp drug abuse/ OR exp substance abuse/ OR abus*.hw,ab,ti. OR exp pregnancy/ OR pregnan*.hw,ab,ti. OR exp pregnancy complications/ OR exp lactation/ OR exp breast feeding/ OR (exp milk human/ and exp secretion/) OR exp fertility/ OR exp reproduction/ OR exp fetus/ OR exp embryo/ OR terat*.hw,ab,ti. OR exp drug efficacy/ OR exp drug withdrawal/ OR exp medication error/ OR exp death/ OR death*.hw,ab,ti. OR fatal*.hw,ab,ti. OR exp drug interaction/ OR exp drug interaction/ OR exp carcinogenicity/ OR carcinogen*.hw,ab,ti. OR mutagen*.hw,ab,ti. OR exp 'off label drug use'/ OR exp occupational exposure/ OR exp toxicity/ OR toxic*.hw,ab,ti. OR pharmacotox*.hw,ab,ti. OR neurotox*.hw,ab,ti. OR cardiotox*.hw,ab,ti. OR nephrotox*.hw,ab,ti. OR immunotox*.hw,ab,ti. OR hepatotox*.hw,ab,ti. OR cytotox*.hw,ab,ti. OR immunocytotox*.hw,ab,ti. OR exp intoxication/ OR exp congenital disorder/ OR exp drug treatment failure/ OR exp case report/ OR case reports.hw,ab,ti. OR exp environmental exposure/ OR exp treatment contraindication/ OR exp drug contraindication/ OR exp injury/ OR suicide.hw,ab,ti. OR exp poisoning/ OR exp *drug tolerance/ OR exp *treatment failure/ OR exp *drug resistance/ OR exp substance-related disorders/ OR exp treatment failure/ OR exp drug resistance/ OR drug resistance.fs.

A look at the relative merits of search filters in a paragraph format vis-à-vis a line-by-line format, using as an example the EMA AE Filter (Part 2).

Background

Generally speaking, search filters, whether displayed on screen or reported in scientific literature come in three formats. These are, firstly the “line-by-line” format where search expressions are entered or displayed as a list, one on top of the other, literally line by line. The second format, here referred to as the “paragraph” format has all the search expressions bundled into a single line that appears as a block of text. This provides for a more compact display, and can in turn, be also run as a single line search. Thirdly, the “hybrid” format describes search strategies that contain a mixture of line-by-line and paragraph format search expressions.

Opting for one format over another depends upon many factors. These vary from available screen space to the capacity of the reporting vehicle, e.g. a printed journal, to simply personal choice.

The purpose of this Focused Search is to raise a note of caution when using the paragraph format without firstly verifying whether or not the search expressions (a). run in the target database, and (b). are relevant to the task at hand. The AE Filter as shown above, unpacked, extends to 60 lines listed line-by-line. This way the relative presence of the terms and phrases can be more easily assessed. As too can be the balance between free term and thesaurus-based searches, and with respect to the latter,  whether they have been exploded. Using Ovid’s Edit function (Actions / More / Edit) a thesaurus expression can have the “exp” command function deleted or added to see what a difference this makes.

It is recommended that your key search filters be saved and stored in both paragraph and line-by-line formats. The former for ease of execution and display. The latter for verification, updating and overall knowledge asset management.  

Ovid Trainer Tips

• Command line Syntax: Lists of search expressions can be neatly combined using the OR operator as displayed in line #61 above, i.e. or/1-60.
• Ovid Search History Launcher Tool: Having unpacked a paragraph formatted search using for example, Notepad, the resulting list of search expressions can be easily imported into Ovid using the Ovid Search History Launcher Tool. See https://tools.ovid.com/ovidtools/launcher.html .
• Share Search History: Conversely, searches regardless of format can be exported from Ovid into other applications for eventual re-use, for peer review and reporting purposes. Located in the Search History section of the Ovid interface, the three Share Search History options are, Email All Search History, Copy Search History Link and Copy Search History Details.

Strategy

exp adverse drug reaction/

adverse.hw,ab,ti.

side effect.hw,ab,ti.

side effects.hw,ab,ti.

side effect.fs.

exp drug overdose/

overdos*.hw,ab,ti.

exp drug misuse/

misus*.hw,ab,ti.

exp drug abuse/

exp substance abuse/

abus*.hw,ab,ti.

exp pregnancy/

pregnan*.hw,ab,ti.

exp pregnancy complications/

exp lactation/

exp breast feeding/

(exp milk human/ and exp secretion/)

exp fertility/

exp reproduction/

exp fetus/

exp embryo/

terat*.hw,ab,ti.

exp drug efficacy/

exp drug withdrawal/

exp medication error/

exp death/

death*.hw,ab,ti.

fatal*.hw,ab,ti.

exp drug interaction/

exp drug interaction/

exp carcinogenicity/

carcinogen*.hw,ab,ti.

mutagen*.hw,ab,ti.

exp 'off label drug use'/

exp occupational exposure/

exp toxicity/

toxic*.hw,ab,ti.

pharmacotox*.hw,ab,ti.

neurotox*.hw,ab,ti.

cardiotox*.hw,ab,ti.

nephrotox*.hw,ab,ti.

immunotox*.hw,ab,ti.

hepatotox*.hw,ab,ti.

cytotox*.hw,ab,ti.

immunocytotox*.hw,ab,ti.

exp intoxication/

exp congenital disorder/

exp drug treatment failure/

exp case report/

case reports.hw,ab,ti.

exp environmental exposure/

exp treatment contraindication/

exp drug contraindication/

exp injury/

suicide.hw,ab,ti.

exp poisoning/

exp *drug tolerance/

exp *treatment failure/

exp *drug resistance/

exp substance-related disorders/

exp treatment failure/

exp drug resistance/

drug resistance.fs.

or/1-64

How run a search history to locate references to information retrieval topics and set it up as an AutoAlert.

Background

Sponsored by the European Commission, the European Network for Health Technology Assessment (EUnetHTA) was set up to bring together the Health Technology Assessment (HTA) Agencies across the EU, to exchange experience and develop practice as well as methodological guidelines.

One of the project outcomes has been the publication of a methodological guideline entitled, Process of information retrieval for systematic reviews and health technology assessments on clinical effectiveness. Comprehensive, systematic and helpfully readable, this publication is highly recommended to information specialists and medical librarians working on systematic review. The authoring team comes from IQWIG in Germany, NIPH in Norway and AETSA in Spain.

This Focused Search draws upon a search strategy, described in Annex 2 of the EUnetHTA methodological guideline, which retrieves references that discuss information retrieval topics. These can range from accounts of experience gained by varying user groups using search techniques to reports of interactions with specific resources, for example PubMed and Google Scholar.  

Of use to librarians and information specialists keen to monitor developments in the field of information retrieval, the search can be stored in an Ovid My Workspace account and be run manually at intervals determined by the user. Alternatively, the search strategy can be set up as an AutoAlert and run daily, weekly, monthly, or following a database update, as you please. If you would like some assistance from an Ovid Trainer on how to set up this search strategy as an AutoAlert, please request an Ovid Coaching Session.

Strategy

(Semi-automated or data mining or (Capture adj3 recapture) or machine learning).ab,ti.

(search adj3 (strateg* or term* or filter*)).ab,ti.

(query or queries).ab,ti.

search*.ti.

or/1-4

exp "Information Storage and Retrieval"/

"Medical Subject Headings"/

"Abstracting and Indexing as Topic"/

Documentation/

reporting.ab,ti.

(bibliographic databas* or Pubmed).ab,ti.

(MeSH or controlled vocabulary or indexing).ab,ti.

or/6-12

"Review Literature as Topic"/

exp "Evidence-Based Practice"/

"Technology Assessment, Biomedical"/

or/14-16

and/5,13,17

exp *"Information Storage and Retrieval"/

4 and (16 or 19)

(Medline or PubMed).ti.

(Clinical Queries or Haynes or hedge or search).ti,ab.

and/21-22

or/18,20,23

How to check for thesaurus term compatibility. An example using the entry term adverse drug event on Ovid MEDLINE and then on Embase on Ovid.

Background

When running search strategies in Embase on Ovid, that were originally designed in Ovid MEDLINE, care needs to be taken to ensure they are delivering the required information as expected. Although there is clear kinship between the two thesauri, MeSH and Emtree, they are nevertheless different in terms of their structure, editorial processing and subsequent operation.

This Focused Search demonstrates how the phrase adverse drug event submitted as an entry term into the Advance Search on Ovid MEDLINE is mapped onto the MeSH term "Drug-Related Side Effects and Adverse Reactions". As adverse drug event is a “used for” term for the MeSH term "Drug-Related Side Effects and Adverse Reactions", entering adverse drug event/ , i.e. with a backslash which forces Ovid to perform a thesaurus search, this search expression yields the same result. See lines #1 and #2 in the screen shot below.

Ovid MEDLINE < 1946 to Present >

However, when we re-run the same search expressions in Embase on Ovid, they execute seemingly without a problem and yield results. The MeSH term "Drug-Related Side Effects and Adverse Reactions" is “understood” by Embase. But, from a returned results point of view, not in the same way as entering the phrase adverse drug event when in Embase on Ovid and have Embase map the entered expression onto the Emtree thesaurus. Compare lines #1 and #2 below.

Embase <1974 to Present>

Although Ovid MEDLINE to Embase on Ovid searches appear to function seamlessly in an operational sense, in terms of being informationally useful, further assumption checks and testing may be needed.  

Strategy

"Drug-Related Side Effects and Adverse Reactions"/

[ Entry term is 'adverse drug event', term is mapped to MeSH ]

adverse drug event/

[ Entry term is 'adverse drug event/' ,i.e. ends with a backslash ]

adverse drug event.mp.

[ Entry term is 'adverse drug event.mp.' ,i.e. runs an multi-purpose fields' search ]

docz.dz. [ Now go to Change below, select Embase and re-run the above search in Embase on Ovid ]

How to localise search queries to regions when geopolitical as well as population-based definitions are meant as opposed to purely geographical definitions.

Background

The MEDLINE view of regions is decidedly geographical. The MEDLINE controlled vocabulary, MeSH, describes Europe as, “The continent north of AFRICA, west of ASIA and east of the ATLANTIC OCEAN.”

The exploded MeSH term exp Europe/ reflects this vast geographical expanse. However, there may be occasions where a narrower definition of a region is preferred. For example, “Europe and the UK”. In this real-life example, further qualification discussions established that “Europe”, for the purposes of the investigation, was understood to be the countries making up the European Union.

This Focused Search, presented here as a search block, consists of 4 search lines, the search expressions compacted into the paragraph format for ease of viewing. Line #1 represents the countries making up the EU, individually selected from the geographical classification as rendered by MeSH. Line #2 locates countries by their English name using free term searching in the .ti,ab,hw,kf, fields for Ovid MEDLINE. Line #3 on the other hand identifies nationalities by their English name or names using free term searching also in the .ti,ab,hw,kf, fields for Ovid MEDLINE. Line #4 combines the controlled vocabulary terms (#1) and the two free term searches (#2 plus #3) with the OR operator so as capture both MEDLINE indexed records as well as those not indexed or in the process of editorial review.

Strategy

europe/ or austria/ or belgium/ or exp baltic states/ or bulgaria/ or croatia/ or czech republic/ or hungary/ or poland/ or romania/ or slovakia/ or slovenia/ or exp france/ or exp germany/ or exp united kingdom/ or greece/ or ireland/ or exp italy/ or luxembourg/ or exp mediterranean islands/ or netherlands/ or portugal/ or "scandinavian and nordic countries"/ or exp denmark/ or finland/ or iceland/ or sweden/ or spain/

(Austria or Belgium or Bulgaria or Croatia or (Republic adj2 Cyprus) or Czech Republic or Denmark or Estonia or Finland or France or Germany or Greece or Hungary or Ireland or Italy or Latvia or Lithuania or Luxembourg or Malta or Netherlands or Poland or Portugal or Romania or Slovakia or Slovenia or Spain or Sweden or Great Britain or Northern Ireland).ti,ab,hw,kf.

(Austrian$1 or Belgian$1 or Bulgarian$1 or Croatian$1 or Croats or Cypriot$1 or Czech or Danish or Estonian$1 or Finnish or French or German$1 or Greek$1 or Hungarian$1 or Irish or Italian$1 or Latvian$1 or Lithuanian$1 or Luxembourger or Maltese or Dutch or Polish or Portuguese or Romanian$1 or Slovak$1 or Slovenian$1 or Spanish or Swedish or British or Northern Irish).ti,ab,hw,kf.        

1 or 2 or 3

Focused Searches by Topic: Natural Disasters & Public Health

Background

This search locates records about tsunamis, tidal waves and earthquakes and types of disaster planning. Earthquakes beneath the sea, or near the shore are often accompanied by destructive waves.

All the MeSH terms (followed by /) in the search are established subjects, but the keyword elements (.mp.) use the question mark truncation symbol (?) to disguise whether the word or phrase may be singular or plural (by including an “S” suffix). The $ or * truncation symbol is also used as unlimited truncation, so aftershock$ matches with aftershock or aftershocking.

Keyword searches use the author’s words from the title and abstract or author keywords (.ti,ab,kw.), as well as selected subjects fields from the database.

Strategy

exp Earthquakes/ or (earthquake$ or aftershock$).ti,ab,kw.

Tsunamis/ or tsunami?.mp.

Tidal Waves/ or tidal wave?.mp.

1 or 2 or 3

exp Emergency Medical Services/ or exp disease outbreaks/

disaster planning/ or emergency shelter/ or mass casualty incidents/ or medical countermeasures/ or relief work/ or rescue work/

5 or 6

4 and 7

limit 8 to (yr="2015 -Current" and "humans only (removes records about animals)")