Funk and Beck "Driving Use: Identifiers and Enhanced Metadata"
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This presentation was provided by Kathryn Funk of The U.S. National Library of Medicine (NIH), and Jeff Beck of The National Center for Biotechnology Information (NCBI), during the NISO Event "Open Access: The Role and Impact of Preprint Servers," held November 14 - 15, 2019.
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Funk and Beck "Driving Use: Identifiers and Enhanced Metadata"
- 1. Driving Use of Preprints: Identifiers and Enhanced Metadata Jeffrey Beck – Program Head, Literature Kathryn Funk – Program Manager, PubMed Central
- 2. NIH intends to maximize impact of interim research products that are developed with NIH funds. National Institutes of Health, March 24, 2017 https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-050.html
- 3. Awardees are encouraged, not required, to post preprints. Applicants are not required to cite preprints as part of their grant applications. Preprints do not fall under the NIH access policy. A few notes on NIH’s Position https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-050.html
- 4. Make preprint publicly available Acknowledge NIH funding Clearly state work was not peer reviewed Declare any competing interests Select CC-BY or public domain license Choose repository that follows best practices NIH Expectations for Researchers Who Post Preprints
- 5. How to maximize impact and drive use?
- 6. NIH Guidelines for Selecting Preprint Servers https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-050.html Image: Open Science Basics, CC0 https://book.fosteropenscience.eu/en/02OpenScienceBasics/02OpenResearchDataAndMaterials.html
- 7. PMC nlm’s open literature archive Launched in February 2000 Digital counterpart to NLM’s print collection Collaboration with subscription and open access journals as well as research funders All content stored in archival standard XML format (JATS) Repository for peer-reviewed accepted manuscripts supported by NIH since 2005
- 8. Europe PMC Operated by EBI Currently includes preprint citation and abstract metadata sourced from Crossref (bioRxiv, ChemRxiv, PeerJ Preprints, and F1000Res). PubMed Central Operated by NLM Currently does not include preprints Considering pilot to ingest preprints citing NIH support PMC International Network
- 9. PID Article Title Article Type Authors Copyright License Funding Publisher COI Journal Articles Preprints Journal info Volume Issue Server or platform info Preprint indicator Version indicator Standardized Metadata
- 10. PID Article Title Article Type Authors Copyright License Funding Publisher COI Journal Articles Preprints Journal info Volume Issue Server info Preprint indicator Version indicator Standardized Metadata
- 11. PID Article Title Article Type Authors Copyright License Funding Publisher COI Journal Articles Preprints Journal info Volume Issue Server info Preprint indicator Version indicator Standardized Metadata
- 12. PID Article Title Article Type Authors Copyright License Funding Publisher COI Journal Articles Preprints Journal info Volume Issue Server info Preprint indicator Version indicator Standardized Metadata
- 13. Preprints, Servers, & Publishers • Preprint server as <journal-title> • <publisher> metadata should identify organization responsible for server Who is providing the hosting and taking responsibility for addressing concerns re: plagiarism, competing interests, misconduct? Who is taking responsibility for ensuring hallmarks of reputable scholarly publishing are rigorous and transparent?
- 15. Preprint Indicator <article article-type="research-article" dtd-version="1.2" xml:lang="en"> <front> <journal-meta> >...</journal-meta> <article-meta> <article-version article-version-type=“status” >preprint</article-version> ... </article-meta> </front> <body>...</body> <back>...</back> </article>
- 16. Preprint Version Control Recommend extending ICMJE recommendations regarding correcting published articles to preprints, Post a new version with details of the changes from the original version and the date(s) on which the changes were made. Archive all prior versions of the article. Previous electronic versions should prominently note that there are more recent versions of the article. The citation should be to the most recent version. http://www.icmje.org/recommendations/browse/publishing-and- editorial-issues/corrections-and-version-control.html
- 17. Persistent Identifiers and Versions “Talking AboutVersions” (Crossref Document) https://docs.google.com/document/d/13L29 Euis2uruRb3LTypnKHuPTB86Um8jRqDV5h_ CcXg/edit Preprints are intellectually distinct from the peer-reviewed paper accepted for publication in a journal, and as such should have a unique Crossref currently recommends a new DOI for each version of the preprint.
- 18. Article Stacks Version 1 Version 2 Version 3 Version 4 Version 1 Version 2 Retraction Updates and Corrections Retraction • Each article (stack) has one ID (DOI) • Systems need to resolve the article ID to the latest version available • All versions should be available from every other version • Each version should include the change log from the previous and the pub date of that version and the original pub date of the article. A retraction is the end of the line for this article!
- 19. Preprint Stacks Version 1 Version 2 Version 3 Version 4 Version 1 Version 2 Withdrawal Notice Updates and Corrections Withdrawal • Each preprint (stack) has one ID (DOI) • Systems need to resolve the PUID to the latest version available • All versions should be available from every other version • Each version should include the change log from the previous and the pub date of that version and the original pub date of the article. A withdrawal is the end of the line for this preprint!
- 20. Ensuring Integrity and Transparency Facilitate linking from preprint to version of record / published version by including preprint PID/DOI in article metadata. (NIH expectation) Establish best practices for maintenance of the scientific record, e.g., withdrawals or retractions to deal with plagiarism or scientific misconduct. (NIH expectation) Build a common vocabulary for preprints, e.g., publishing vs. posting, that can enable more productive discussions around standards.
- 21. Thank You! Special thanks to our colleagues at Europe PMC who kindly shared their expertise and experiences with preprints: • Michele Ide-Smith • Michael Parkins • Jo McEntyre … and NLM colleagues and leadership who have supported our engagement with the preprint community: • Patricia Brennan • Jerry Sheehan • Jim Ostell • Kim Pruitt • Chris Kelly This research was supported by the Intramural Research Program of the NIH, National Library of Medicine.
Editor's Notes
- Why are we interested in driving use of preprints? In 2017, NIH began encouraging investigators to use interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work.
- For NIH researchers that opt to post preprints, NIH provides some general guidelines, which we’ve taken into account into account in our later recommendations where applicable.
- With these expectations in mind, the question becomes how can NIH maximize impact and drive use of preprints?
- One way, NIH has approached this is by laying out clear guidelines for researchers to use in selecting preprint repositories. A number of these guidelines tie in directly to the recommendations we’ll be looking at around metadata and standards for supporting use, including content that is findable, accessible, interoperable and re-usable, encouraging researchers to post preprints to servers that make the content and metadata open, and easy to access by machines and people. This access is both a function of permission (e.g. use of Creative Commons licenses) and technology (e.g. application program interfaces).
- Building on the FAIR principles and the NIH guidelines, another way to maximize impact and drive use is to facilitate discovery of preprints and ensure long-term preservation and access this content. To that end, NIH has looked to NLM to explore how we can leverage our existing literature databases, such as PubMed Central, for this purpose. As NLM’s free full-text archive of biomedical and life sciences journal literature, PMC serves as a digital counterpart to NLM’s extensive print journal collection and has been an archive of NIH-funded peer-reviewed literature since 2005. PMC stores all content in the archival XML standard for journal articles, JATS, and provides machine-readable metadata to PubMed to facilitate discovery of its contents. PMC currently collects journal versions of record directly from publishers as well as peer-reviewed, accepted author manuscripts that fall under the public access policies of NIH and a number of other public and private research funders.
- To help non-US funding organizations build national or regional repositories of funded research articles, NLM has established the PMC International Network, which includes Europe PMC. PMC International sites mirror content held in PMC, but may also supplement their collections with other materials of particular interest to their respective communities that may fall outside the scope of US PMC and the NLM Collection. As a result of the freedom to supplement collections, Europe PMC began ingesting preprint citation and abstract from CrossRef in July of 2018 Conversely, at this time, US PMC has not started incorporating any preprint content, but is considering a pilot to archive the full text of preprints acknowledging NIH support in PMC and make them discoverable in PubMed.
- For databases such as PMC and Europe PMC, facilitating the discoverability and use of preprints is dependent on the application and distribution of consistent metadata, much of which is consistent with article-level metadata associated with journal articles. To that end, in preparing for this presentation, what we tried to do was see where we could leverage existing the journal article metadata model as defined by the Journal Article Tag Suite, and identify the areas of overlap as well as potential points of divergence between articles and preprints.
- There are of course the standard metadata elements for papers that are key, such as a PID, title, and authors, to the citation and discovery of research objects.
- Additionally, the standardized capture of funding metadata is a critical element in allowing funders to track the impact of the research they support. Funders are also invested in ensuring that conflicts of interests are made open to ensure the integrity of the research they support.
- Most of the rest of the presentation will focus on these areas where the metadata for preprints may diverge from traditional articles in order to ensure the transparency and integrity of the scholarly record. We found that metadata elements seem to diverge when it comes time to account for the less formal (for lack of a better term) nature of preprints. We needed to determine how to account for capturing server information, whether peer-review status needed to be captured or if there was an acceptable proxy to use, and maintenance of a potentially many-versioned publication record. We also needed to sort through where the concept of ‘publisher’ fit into this picture.
- In reviewing NIH guidelines for researchers, which note that preprint servers should have policies for addressing concerns regarding plagiarism, competing interests, and scientific misconduct and ensuring scholarly publishing practices are transparent followed, we decided the metadata should include the organization taking responsibility for posting and enforcing such policies. We recommend the preprint server be identified as <journal title> and the <publisher> field name the organization responsible for enforcing the policies and practices of the server.
- Another NIH guideline or expectation is that preprints be transparent and clearly indicate a preprint and or ‘not peer reviewed status’. We do not consider peer review status to be metadata (consistent with journal articles that are not peer reviewed); though we also do not want to rely solely on platform or server as a proxy for identifying preprints. In some cases, such as the publishing model used by F1000 Research, a paper could have a preprint status or be a peer reviewed article within the same publication at different points of time. So in lieu of machine-readability and rendering of preprint status there needs to be some sort of indicator that users and discovery systems can queue off of.
- A preprint indicator should not be confused with @article-type, which should continue to reflect the type of paper being posted, i.e., original research, review, editorial, etc.
- Perhaps the most significant challenge in capturing metadata for preprints is version control.