Author Archives: Dina

New Preprint-related Developments at eLife

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Since the COVID pandemic, preprint servers have become increasingly accepted within the publishing landscape, with even literature databases (like PubMed and Scopus) taking on the task of selectively indexing some of this new type of “not-yet-confirmed by peer-review” content. No doubt, since preprint servers are outlets for “the distribution of preprints that are complete but unpublished manuscripts describing health research”, this has been a big step for scholarly research database providers.

The increased popularity of preprints has also inspired both scholarly publishers and other research stakeholders to start re-imagining how the scientific research peer-reviewed publishing process in general might be improved now that preprints are often in the mix. For example, the publishers of the open access journal eLife, who have been actively trying to bring on the evolution of publishing by experimenting with new publishing processes/models since their inception 10 years ago, have made some noteworthy changes related to preprints over the last two years that are worth paying attention to.

In a rather radical move, in July 2021, eLife began ONLY reviewing manuscripts that had already been posted as preprints (on bioRxiv or medRxiv), deciding to “focus its editorial process on producing public reviews to be posted alongside the preprints”. Fast-forward 18 months, and starting in January 2023, the eLife editorial process will altogether “eliminate accept/reject decisions after peer review and instead provide readers with richer and more nuanced assessments of articles”, which they will call “eLife assessments”. In short, every preprint that is sent out for review by eLife editors will be published as a “Reviewed Preprint”, after which the authors may choose to undertake revisions and will be involved in deciding which manuscript version will become the final version of record (ie. the final published version that will be indexed in scholarly databases).

Note: These are just the “headline” highlights – to learn more in-depth details about eLife’s new publishing process, be sure to read:

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.

PubMed Central (PMC) Related Resources Feature

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In March of 2022, PMC launched its updated interface, which was intentionally designed to offer a familiar search experience for regular users of the new PubMed website (released in 2020). Learn more about the New PMC Website from NCBI Insights.

At the end of August 2022, they continue to add features that are much-appreciated by users of PubMed, namely the “Related Resources” functionality that is now available in both tools on the individual article record level. The PMC Related Resources feature includes three sections that a user may choose to expand and explore: 1) Similar articles, 2) Cited by other articles, and 3) Links to NCBI databases.

Below is the view of the Similar articles section expanded for a PMC article:

From the NLM Technical Bulletin:

PMC Releases Improved Related Resources Feature. NLM Tech Bull. 2022 Jul-Aug;(447):e4.

“Section 1: Similar articles. When expanded, this section displays a snapshot of articles from the PubMed database that are closely related to the one you are currently viewing (see Figure 2). The title, journal, and publication year of each article are displayed. You can click on an article title to navigate to its record on the PubMed site or click the “See all in PubMed” link to see the full list of similar articles in PubMed. When no similar articles are found, you’ll see a “No results available” message.

Section 2: Cited by other articles. When expanded, this section displays a snapshot of articles from the PubMed database that cite the article you are currently viewing. The title, journal, and publication year of each article is displayed. You can click on an article title to navigate to its record on the PubMed site or click the “See all in PubMed” link to see a full list of articles from PubMed that cite the one you are viewing. When no articles are found in PubMed that cite the article, you’ll see a “No results available” message.

Section 3: Links to NCBI databases. When expanded, this section displays links to records in other NCBI databases that relate to the current article you are viewing. You can click on the name of the NCBI database to navigate to a related record in that database. When there are no links to other NCBI databases available for the current article, you’ll see a “No results available” message.”

Questions? Ask Us at the MSK Library!