Author Archives: Dina

Making Research Data Available on Mendeley Data When You Publish in an Elsevier Journal

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Most people who are familiar with Mendeley know it as the web-based citation manager that has been around for about 15 years (owned by Elsevier since 2013) and that MSK now has an institutional subscription to. Another Elsevier product, Mendeley Data, was released in April 2016 and is “an open, free-to-use research data repository, which enables researchers to make their research data publicly available.” The tool is freely-available to researchers in all disciplines and can be used to share unpublished data privately within a research team or to upload and publish data linked to/from a published journal article.

From Elsevier Support:

“Many Elsevier journals now offer authors the ability to submit research data as part of the article submission process, and research datasets submitted in this way will be stored and independently available on Mendeley Data, linked to/from your published article. The Guide for Authors for the journal you are planning to submit to will indicate if this is available.”

For an example of what this looks like in practice – see:

Article: https://pubmed.ncbi.nlm.nih.gov/34375669/

    • Stewart JR, Lang ME, Brewer JD. Efficacy of nonexcisional treatment modalities for superficially invasive and in situ squamous cell carcinoma: A systematic review and meta-analysis. J Am Acad Dermatol. 2022 Jul;87(1):131-137. doi: 10.1016/j.jaad.2021.07.067. Epub 2021 Aug 8. PMID: 34375669.

Dataset: https://data.mendeley.com/datasets/dcvzp8y5g4/1

    • Stewart, Jacob; Lang, Margaret; Brewer, Jerry (2021), “Non-excisional treatment of SCC and SCCIS Supplemental”, Mendeley Data, V1, doi: 10.17632/dcvzp8y5g4.1

There are multiple advantages to having the option of making datasets available on Mendeley Data, including overcoming some annoying realities of using scholarly literature. First, not all journals are able to provide authors with unlimited space to share their research data – whether that is within the published article or within the Supplemental Materials section/Appendices (which may or may not be available as an option). Second – if the journal is behind a paywall and not openly-available, the supplemental materials will generally need to be obtained by the reader (who does not have access to a paid subscription) separately via inter-library loan (ILL) if the datasets are needed since article supplemental materials are not typically obtained by default via ILL, only by special request.

As such, having an open, independent place online where readers can easily access any related datasets makes it more likely that they will go to them if a question arises when they are reading the research paper. Also, Mendeley Data assigns published datasets persistent DOIs (digital object identifiers) and provides usage metrics thanks to integration with Plum Analytics. Furthermore – all published datasets in the repository can be searched and discovered independent of the published paper as each dataset has its own metadata, making it more likely to be found and potentially re-used/properly cited by other researchers.

Learn more:

Swab, M. Mendeley Data (2016). Journal of the Canadian Health Libraries Association, 37 (3), pp. 121-123. https://journals.library.ualberta.ca/jchla/index.php/jchla/article/download/28162/20988

Garcia Morgado, J.Open data – How to make the data available with Mendeley Data
(2019) XVIII Workshop REBIUN de Proyectos Digitales/VIII Jornadas OS Repositorios
September 25-27, 2019, León [Online]. Available at https://buleria.unileon.es/handle/10612/11221

Haak W, García Morgado J, Rutter J, Zigoni A, Tucker D. Mendeley Data. Research Data Sharing and Valorization: Developments, Tendencies, Models: Wiley; 2022. p. 153-73.
https://onlinelibrary.wiley.com/doi/abs/10.1002/9781394163410.ch9

Questions? Ask Us at the MSK Library!

Systematic Bulk Downloading of Articles from PubMed Central (PMC)

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In this era of artificial intelligence (AI) and machine learning (ML), there is increased interest in accessing large numbers of full-text articles to train deep learning models and/or evaluate their performance. The U. S. National Library of Medicine (NLM)’s PubMed Central (PMC) full-text article repository is a popular choice with AI/ML researchers who are often looking for a free, openly accessible source of the scholarly biomedical literature. For a recent example of research carried out using the PMC Open Access Subset, see PMID: 37094464:

Although the NLM is generally accommodating of researchers using and even building upon all the tools and resources that it develops and supports, there is an expectation on the part of NLM that researchers will work within their rules and restrictions. Anyone interested in “automated retrieval of articles in machine-readable formats in PubMed Central (PMC)” is encouraged to explore the “several large datasets of journal articles and other scientific publications made available for retrieval under license terms that generally allow for more liberal redistribution and reuse than a traditional copyrighted work (e.g., Creative Commons licenses)”. However, there are “Restrictions on the Systematic Downloading of Articles”– see https://www.ncbi.nlm.nih.gov/pmc/tools/textmining/. 

When researchers try to bulk download a large amount of content via the regular PMC web interface on their own, PMC’s systems notice the increased activity and block the IP range(s) responsible as this is in violation of the terms of the PMC Copyright Notice which states that “Systematic downloading of batches of articles from the main PMC web site, in any way, is prohibited because of copyright restrictions.”

From: https://www.ncbi.nlm.nih.gov/pmc/about/copyright/:

PMC makes certain subsets of articles (i.e., the PMC Article Datasets) accessible through auxiliary services that may be used for automated retrieval and downloading. These are:

These services are the only services that may be used for this purpose. Do not use any other automated processes for downloading articles, even if you are only retrieving articles from the PMC Article Datasets (including the PMC Open Access Subset).

Questions? Be sure to Ask Us at the MSK Library!

NEW EndNote Web for EndNote 21 Users

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Now that EndNote 21 is available at MSK, users may wish to take advantage of the new EndNote Web tool which is included as part of MSK’s institutional license for the EndNote 21 desktop version. The most important takeaway to remember about the new EndNote Web is that it is NOT in any way intended to be used “on its own” as a substitute for the EndNote 21 desktop version. Rather it is intended to add flexibility to the EndNote 21 desktop user experience by making it possible for users to access their EndNote library from anywhere.

As per Clarivate’s marketing:

“With EndNote you can access your research anytime, anywhere online. Move seamlessly between online and the desktop and iPad applications in the cloud.

Say hello to the brand-new EndNote Web, available only to EndNote 21 customers for three years from activation date. Securely sync your entire library including PDF’s, notes, and annotations across all your devices.”

“EndNote Web has been redesigned from the ground up” 

What this means in practical terms is that EndNote Web on its own no longer functions as a complete citation manager but is basically a cloud storage solution for the EndNote 21 desktop tool. Users are expected – for the most part – to make their references available in EndNote Web by syncing from the desktop tool. That said, references can also be imported into EndNote Web from a file or created manually, added to a group, exported, or deleted.

Furthermore, an EndNote library can now be shared with up to 1,000 colleagues. However, the actual sharing action needs to be carried out in the desktop version of EndNote (by going to File > Share, and then adding the email addresses of colleagues who will be given access). Individuals can be assigned either “Read Only” or “Read-Write” privileges, giving the EndNote desktop library account owner the ability to decide who can simply access the references versus who can make changes to their EndNote Web shared library.

Also, when working on writing up their research, users now can insert their EndNote references into more word processing software options: Microsoft Word™, Apple Pages™ and Google Docs™. Cite While You Write (CWYW) plug-ins/add-ons are available for download, for example – see: EndNote: Google Docs CWYW (clarivate.com). (Tip: If you have the EndNote 21 tab installed in MS Word, you can go to Preferences > Application tab to specify if you wish for MS Word to draw from your desktop EndNote library, from your new EndNote Web library, or from your EndNote Online Classic library.)

NEW EndNote Web is completely different than EndNote Online Classic

Because the vendor realizes that EndNote Web and EndNote Online Classic are quite different tools, Clarivate will continue to make both tools available. Users who already have an EndNote Online Classic account may log into EndNote Web using the same online credentials if they want  their online references from the classic tool to be available in the new online tool. However, they are also welcome to sign-up for a brand new account.

The reason why Endnote Online Classic is so different than the new EndNote Web is that it was developed with a completely different purpose in mind, many years ago. Back then, it was described by the company as “the online counterpart to our popular desktop reference management and bibliography creation software” that was available as a free basic version (i.e. with much less functionality than the desktop version). From the vendor’s handout:

“Whether you use EndNote online through Web of Science™, with EndNote desktop, or on its own – you reduce the time you spend searching, updating, and cleaning your research and formatting documents. Depending on how you access EndNote online, you may see different features and options. > ENDNOTE BASIC If you only have access to EndNote online, and not EndNote desktop, you are considered a basic user. While your feature set is limited compared to those using EndNote online in addition to the desktop, it’s still perfect for the new-to-research and writing student.”

For years, EndNote Online Classic served as an introductory student gateway to more sophisticated citation management tools, as well as a vehicle for sharing references between colleagues. Currently, the classic online version can still be used independently as a basic tool for capturing and managing references (that even allows for online searching of tools like PubMed for harvesting new citations) but it likely will not be further developed by the vendor. 

EndNote Online Classic User Guides:

https://clarivate.libguides.com/ld.php?content_id=64075557

https://endnote.com/wp-content/uploads/m/pdf/en-online-qrc.pdf

https://endnote.com/product-details/compare-current-versions

Questions? Be sure to Ask Us at the MSK Library!