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White Paper: Regulatory Implications of New Pubmed Introduction academic research and R&D in a variety of industries. Consequently, “PubMed listed” PubMed is a widely-used articless have become a academic search database in byword for quality, peer- both academia and a number reviewed works, the of industries. Whilst it is not the importance of which has only academic search grown in recent years with the database, it is widely used in rise in the number of predatory the life and physical sciences journals. due to its ease of use and rapid access to MEDLINE journals, and it is considered a PubMed & MedTech repository for quality peer- reviewed publications. For the medical device and in vitro diagnostic industry the ability to perform specific and About PubMed repeatable searches of a reputable academic database is an invaluable tool for a wide variety of processes. As well as Made available by the being useful for product design National Center for and development, the Biotechnology Information identification of critical (NCBI), PubMed is a free evidence for scientific validity, resource to assist in the as well as analytical and identification of biomedical, clinical performance, is critical life- and physical-science- for a range of regulatory based academic literature, processes, not least of all risk containing over thirty million management and clinical or abstracts and citations. performance evaluation. PubMed has been publicly available since 1996 and, due When utilised as part of the to its easy access, user-friendly clinical evaluation or interface and curation by the performance evaluation well-respected NCBI, it has processes, either within the become a mainstay of. clinical evaluation report (CER) 02 The biggest change users are likely to notice is that the new PubMed will likely increase the number of returned hits or performance evaluation report (PER) themselves, or as compared with the previous part of subsequent proactive version of the platform. surveillance of the literature in This is likely due to: the post-market phase (an • Automatic term increasingly important mapping, consideration under the medical device regulation • Removal of the previous (MDR) and in vitro diagnostic limit to six hundred iterations device regulation (IVDR)), when using a wildcard (*) traceability and repeatability search, and of past searches has always • The default search now been important and something ignores Boolean operations auditors regularly check. (AND, OR, etc.), and defers to PubMed’s own “best match” algorithm. New PubMed Regulatory implications of these changes Behind the scenes, PubMed has been completely rebuilt into a cloud-based service Returning a different number of utilising Solr and MongoDB search results can be search and database problematic for a number of platforms. These changes, reasons: which went live in mid-May • An auditor can no longer 2020, allow for greater verify literature searches scalability for the database made using legacy attributed to its ever-increasing PubMed (i.e. anything with index of literature, whilst at the a literature review carried same time improving reliability out up until mid-May 2020). with the move to the cloud. This is especially important These changes in turn have during clinical audits. allowed new features to be introduced in the search functionality. 03 • New evidence might have been identified that needs appraising prior to a notified can result in a large volume of body review of regulatory returned hits. Taking the documentation. previous example, “sulfation” • Most importantly is the also searches for effect on post-production “dihydrochloride,” which may activities. Both post-market or may not be helpful clinical follow-up (PMCF) depending on the search and post-market being conducted. performance follow-up This effect can be remediated (PMPF) are required to be a by wrapping the terms in “continuous process that quotation marks (“”), which updates the CER/PER” and, eliminates the use of automatic if searches are no longer term mapping. repeatable, the required continuity of the MDR and Alternatively, using the IVDR is lost. advanced option will show the user other suggested terms, which can be added to Remediation of particular search strings using the “OR” function and further searches quotation marks. This is a useful tool for validating existing search methodologies, to Automatic term mapping ensure all valid search terms have been identified. By default, search text is now analysed and there is greater mapping of search terms to Wildcard searches account for factors such as Wildcard (“*”) searches have British vs. American English, always been a useful function. plural forms and synonym However, it was potentially matching. For example, the limiting in legacy PubMed as term “sulfation” will also return only the first six hundred results for “sulphation.” possible iterations were PubMed uses Medical Subject considered. In new PubMed, Headings (MeSH) for synonym however, all possible iterations matching; however, this will be are included. useful in just as many instances as it will be unhelpful, when it If this is undesirable, it can 04 hence, the number of returned hits will differ too, not just the order in which they are presented. This feature can be be one of the more challenging changes to very useful when soft searches resolve. The simplest are performed to freely search the literature. However, it remediation is to simply not use should not be used for highly the wildcard function but, ordered, planned and rather, specify the exact search terms desired. The recorded searches as any automatic term mapping changes to the best match algorithms will make the feature described above can number of hits returned and help identify additional terms the papers change. To remedy that can be utilised and surrounded by quotation marks this simply change the display to ensure a sufficiently wide net option to “publication date” or “most recent.” is being cast. If the wildcard is being used, it is important to remember there may now be a less-specific Replicating previous search than if it was not used. searches The use of the wildcard function also prevents automatic term mapping. Replicating historical searches is an important regulatory Best match algorithm function, one often undertaken By default, the new PubMed by regulatory stakeholders interface sorts search results by during clinical evaluation “best match.” This functionality audits. In order to avoid any can potentially be misleading potential issues when looking to as it is not just changing the repeat legacy searches, way the results are ordered as legacy PubMed is currently still the name may imply. The “best available although, as of mid- match” feature uses machine May 2020, new citations will not learning algorithms to return be added. It can be accessed the most relevant citations at using this link: the top of the results. However, it can also ignore Boolean https://pmlegacy.ncbi.nlm.nih.gov/ operators (AND, OR, etc.); 05 An important thing to note, however, is that simply without its limitations. For changing the date range or instance, if a citation is added applying the publication date without its abstract, without full filter to include the date when term matching, or if the term the original search was carried matching is updated, the out will not necessarily result in results will not appear when the the same number of hits. This is search is performed but will because there can be a slight when the search is repeated in delay between the publication the future. This is particularly of a paper and when PubMed pertinent when there is an assigns that paper a unique unusually high volume of identifier (known as a PubMed literature being published on a ID). If the original search was particular topic in a relatively conducted between these two short space of time, such as dates, a paper may appear on during the COVID-19 a repeated search that did not pandemic. appear on the original search, as the publication was prior to the search date but the How can we help? PubMed ID was assigned after the search date. This can be resolved by using At SciMed, we have a strong the Entry Date, formerly the background in academic Entrez Date, function. This science and regulatory affairs function can be used by across a broad range of medical adding : device and in vitro diagnostic risk classifications and technology areas. AND (YYYY/MM/DD:YYYY/MM/DD [EDAT]) We hope that the white paper has provided you with the where the two dates refer to information you need to the start and end dates of the navigate around New PubMed period being searched. This will and understand how it performs recreate the original search as differently. it would have displayed on the original search date. Although the EDAT function is the most We are always happy to discuss commonly used date filter for such issues, so feel free to reproducible searches it is not contact us or visit https://www.scimedconsult.com to see our wider service offerings and other free resources. 06 SciMed Consultancy Ltd e| [email protected] w| www.scimedconsult.com/resources @SciMedConsult @scimedconsult SciMed Consultancy Ltd a proud member of 2019 Best Medical Device the association of Compliance Consultancy - UK British HealthTech Industries.
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