Tag Archives: systematic reviews

ClinicalTrials.gov – Discovery Tool and Research Data Source

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As ClinicalTrials.gov celebrates its 25th anniversary, reaches its half-million registered studies milestone, and completes its modernization, it’s a good time to appreciate this invaluable research tool that has been around since 2000. In 2008, NLM launched the ClinicalTrials.gov results database, which now (as of 12/2024) has >70K registered studies posted with results.

Openly available to all with “about 90 thousand visitors per day and 2 million unique visitors every month”, ClinicalTrials.gov is a registry where individuals can identify both ongoing and completed registered trials from “50 States and in 229 countries and territories”.

Some functionality that has been added over the last few years (related to how you can search the database using Complex Search Queries and how you can download and use the search results/records from ClinicalTrials.gov) has made this database increasingly attractive as a data source for answering research questions.

From: https://clinicaltrials.gov/find-studies 

In addition to having search functionality that allows for very precise searching, it is now possible to download search results from ClinicalTrials.gov in the RIS file format that can be imported into citation management tools like EndNote and Covidence (used for managing systematic review projects).

It is important to note that the data fields included in the RIS download (which is not customizable), differ from those included in the CSV file download data fields (which a user can select from a menu of options), which differ from the JSON format (which can include every available data field for each study being downloaded). The ClinicalTrials.gov API option allows the ClinicalTrials.gov database to be accessed on a large scale, automated way by researchers and developers.

From: https://clinicaltrials.gov/find-studies/how-to-use-search-results

Examples of research projects that have leveraged ClinicalTrials.gov data:

  1. Alhajahjeh A, Rotter LK, Stempel JM, Grimshaw AA, Bewersdorf JP, Blaha O, Kewan T, Podoltsev NA, Shallis RM, Mendez L, Stahl M, Zeidan AM. Global Disparities in the Characteristics and Outcomes of Leukemia Clinical Trials: A Cross-Sectional Study of the ClinicalTrials.gov Database. JCO Glob Oncol. 2024 Nov;10:e2400316. doi: 10.1200/GO-24-00316. Epub 2024 Dec 2. PMID: 39621951.

  2. Chen D, Parsa R, Chauhan K, Lukovic J, Han K, Taggar A, Raman S. Review of brachytherapy clinical trials: a cross-sectional analysis of ClinicalTrials.gov. Radiat Oncol. 2024 Feb 13;19(1):22. doi: 10.1186/s13014-024-02415-8. PMID: 38351013; PMCID: PMC10863227.

  3. Falade AS, Adeoye O, Van Loon K, Buckle GC. Clinical Trials in Gastroesophageal Cancers: An Analysis of the Global Landscape of Interventional Trials From ClinicalTrials.gov. JCO Glob Oncol. 2024 Aug;10:e2400169. doi: 10.1200/GO.24.00169. PMID: 39173083.

  4. Pearce FJ, Cruz Rivera S, Liu X, Manna E, Denniston AK, Calvert MJ. The role of patient-reported outcome measures in trials of artificial intelligence health technologies: a systematic evaluation of ClinicalTrials.gov records (1997-2022). Lancet Digit Health. 2023 Mar;5(3):e160-e167. doi: 10.1016/S2589-7500(22)00249-7. PMID: 36828608.

  5. Yang A, Baxi S, Korenstein D. ClinicalTrials.gov for Facilitating Rapid Understanding of Potential Harms of New Drugs: The Case of Checkpoint Inhibitors. J Oncol Pract. 2018 Feb;14(2):72-76. doi: 10.1200/JOP.2017.025114. Epub 2018 Jan 3. PMID: 29298113; PMCID: PMC5812307.

Questions? Ask Us at the MSK Library!

Covidence Full-Text PDF Enhancements

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Covidence, the systematic review (SR) project management tool that is available for use by everyone in the MSK community via a site license, has recently introduced some noteworthy improvements related to importing the PDF attachments for the full-text screening stage.

  • You can now export only the records of citations missing the Full-Text PDFs.

Being able to easily extract a list of citations of studies missing full text PDFs does not sound like a game-changing enhancement. However, for SR team members who regularly dedicate hours of work harvesting the full-text PDFs for the Full-Text Screening stage of a project, this functionality will be a huge time-saver.

  • You can now export citations as an RIS file for import into reference manager programs beyond Endnote, including:

    1. Endnote
    2. Cochrane Registry of Studies
    3. Zotero
    4. Mendeley
    5. RefWorks

With an increasing number of citation manager program options available to users, including here at MSK – see Citation Management LibGuide for more details – it is nice to see that Covidence is becoming inter-operable with more tools to better match user preferences.

  • You can now bring in Open Access articles using Unpaywall and automatically upload them when studies move to to the Full Text screening or Data Extraction stages.

With the amount of available Open Access journal content continuously increasing, having the ability to automatically bring in the needed full-text that is openly-available on the web will become even more useful as time goes on. Furthermore, individual PDFs that users have already downloaded can now be brought into Covidence using a convenient drag and drop option, making adding these PDFs to their corresponding citation records on the screening list easier than ever.

  • You can now use the Bulk PDF Upload Tool in conjunction with either Endnote or Zotero.

The Bulk PDF Upload Tool involves a two step process that includes saving a list of citation records as an Endnote XML file after all of the needed PDFs have been harvested into a citation manager. Zotero now also accommodates the “Endnote XML” filetype, helping Covidence once again become more versatile for users who choose to use the Zotero citation manager instead of Endnote.

To learn more about Covidence, be sure to check out these training options or Ask Us at the MSK Library.

PRISMA 2020 Replaces PRISMA 2009

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At the end of March 2021, the PRISMA 2020 guideline update was simultaneously published in five journals, officially marking the replacement of the PRISMA 2009 with the updated PRISMA 2020 guideline:

Page MJ, McKenzie JE, Bossuyt PM, Boutron I, Hoffmann TC, Mulrow CD, Shamseer L, Tetzlaff JM, Akl EA, Brennan SE, Chou R, Glanville J, Grimshaw JM, Hróbjartsson A, Lalu MM, Li T, Loder EW, Mayo-Wilson E, McDonald S, McGuinness LA, Stewart LA, Thomas J, Tricco AC, Welch VA, Whiting P, Moher D. The PRISMA 2020 statement: an updated guideline for reporting systematic reviews.

  • BMJ 2021 Mar 29;372:n71. doi: 10.1136/bmj.n71. PMID: 33782057; PMCID: PMC8005924.
  • Syst Rev. 2021 Mar 29;10(1):89. doi: 10.1186/s13643-021-01626-4. PMID: 33781348.
  • J Clin Epidemiol. 2021 Mar 17:S0895-4356(21)00073-1. doi: 10.1016/j.jclinepi.2021.03.001. PMID: 33789819.
  • Int J Surg. 2021 Apr;88:105906. doi: 10.1016/j.ijsu.2021.105906. Epub 2021 Mar 29.PMID: 33789826.
  • PLoS Med. 2021 Mar 29;18(3):e1003583. doi: 10.1371/journal.pmed.1003583. eCollection 2021 Mar. PMID: 33780438.

Published translations of this guideline into other languages are forthcoming.

For the most detailed description of the new PRISMA 2020 guideline, this accompanying “explanation and elaboration” article was also published:

  • Page MJ, Moher D, Bossuyt PM, Boutron I, Hoffmann TC, Mulrow CD, Shamseer L, Tetzlaff JM, Akl EA, Brennan SE, Chou R, Glanville J, Grimshaw JM, Hróbjartsson A, Lalu MM, Li T, Loder EW, Mayo-Wilson E, McDonald S, McGuinness LA, Stewart LA, Thomas J, Tricco AC, Welch VA, Whiting P, McKenzie JE. PRISMA 2020 explanation and elaboration: updated guidance and exemplars for reporting systematic reviews. BMJ. 2021 Mar 29;372:n160. doi: 10.1136/bmj.n160. PMID: 33781993; PMCID: PMC8005925.

  • For details about the process that was used to develop the PRISMA 2020 update:

    Page MJ, McKenzie JE, Bossuyt PM, Boutron I, Hoffmann TC, Mulrow CD, Shamseer L, Tetzlaff JM, Moher D. Updating guidance for reporting systematic reviews: development of the PRISMA 2020 statement. J Clin Epidemiol. 2021 Feb 9;134:103-112. doi: 10.1016/j.jclinepi.2021.02.003. Epub ahead of print. PMID: 33577987.

Noteworthy Changes in the PRISMA 2020 Update

Among the key PRISMA 2020 guideline changes are: more inclusive wording so that it’s more accommodating to other methods from different fields (ex., methods beyond randomized trials of health interventions); some of the categories have been broken down into more granular sub-items that are more explicit and provide more clarity about what exactly should be reported, some new items and sub-items have been introduced or expanded upon; and some of the items have been slightly re-ordered in the checklist.

The new PRISMA 2020 guideline is meant to reflect the changing reality of the current research climate. For example, now that more people are registering their protocols as is recommended by PRISMA, there is a sub-item added to address the clear reporting of potential protocol amendments. Also – in line with the open science movement, there are sub-items related to reporting about the availability of data and statistical code, etc. Furthermore, with automation tools starting to be considered for use in SRs, more explicit reporting in this area is also recommended, as well as the reporting of conflicts of interest of review authors, something which is becoming a more common requirement in all areas of scholarly publishing.

There also has been an obvious push towards greater transparency in the methods, with recommendations to include the full search strategies and number of results for all information resources searched (which is in accordance with the PRISMA-S extension also published this year), as well as to provide the full citations for all of the included studies and citations for the studies that were excluded at the full-text stage, with reasons.

This latest version of PRISMA also appears to recognize that often in SRs, the synthesis of the results includes the grouping or sub-grouping of studies for the analysis, which the guideline suggests should be better reported upon. PRISMA 2020 makes a more explicit request for the reporting of criteria and processes used to group studies. Related to this, PRISMA 2020 also encourages that the reporting of characteristics and risk of bias be handled not for all included studies as a whole but rather to be considered among sub-grouped studies contributing to each synthesis.


New Tools and Templates for PRISMA 2020

It should be noted that the PRISMA guidelines are recommendations and not every item in the checklist applies to every situation. (In fact, it is for that very reason that PRISMA extensions exist and should still be used in conjunction with PRISMA 2020 as not all of these have been perfectly harmonized as of yet.) As such – this guidance should be viewed as useful suggestions for improving the quality of reporting of a systematic review – keeping in mind, however, that not every item is always applicable and mandatory.

This spirit of flexibility is reflected in the increased template options made available on the PRISMA Statement website to accommodate different scenarios. Both the PRISMA 2020 Checklist and Flow Diagram template options are now available for viewing and downloading. In addition to the PDF and Word templates, Shiny App computer applications have also been created that can be used to more easily generate the completed checklist and flow diagram by inputting data.

To learn more, please view a recent presentation on PRISMA 2020 by the first author (Dr. Matthew Page, Monash University) responsible for the update and feel free to send us your questions at Ask Us at the MSK Library or to explore the Systematic Review Service LibGuide.