Here’s a tip for getting the most out of data extraction in Covidence.
For background, the MSK Library has an institutional account to Covidence, an online software platform used for systematic and other related reviews. Covidence offers teams a collaborative space to screen, appraise, and extract data from articles, and our institutional account means anyone at MSK can use this platform for their review projects.
Once you’re within the Covidence page for your review, you’ll see there are four stages below Review Summary, with Extraction at the end. When you click on Settings to the right of Review Summary, you’ll have the option of selecting between Extraction 1 and Extraction 2.
Both extraction options offer a customizable data extraction template, so which to choose?
Extraction 1 is designed for intervention reviews with a standardized PICO(T) structure, as it offers a structured format for organized data collection, which makes meta-analysis easier. This structure allows it to automatically fill in data extraction fields with suggestions you can review. Results can be exported to CSV, Excel, and RevMan.
Extraction 2 offers an unstructured format for flexible data collection and is fully customizable. It doesn’t offer automated extraction suggestions and only exports to CSV.
Learn more about data extraction and templates for these two options in the Covidence Knowledge Base. If you prefer to be hands-on, Covidence offers a demo review, and you can test both extraction options there before choosing which one is best for your project.
Learn more about reviews, Covidence, and the way MSK librarians can support you within the guide to our Systematic Review Service.
When you enter a phrase into PubMed without using quotation marks, the database does several things:
Looks for the phrase as a subject heading, or MeSH, term. Subject headings have been preselected by the database and are assigned to each citation on a topic.
Breaks apart the phrase and looks for each word separately.
Sometimes, this process brings back the results you need. But it can also lead to search results that do not match your topic.
What happens when you search using quotation marks?
Instead of looking for matching subject headings, PubMed checks for the phrase in its phrase index, a list drawn from the literature included in the database.
Not every phrase is included in the phrase index. If your phrase is not found, PubMed may ignore your quotation marks and follow the search steps above, bringing in irrelevant results.
You can see how many results include your phrase from the advanced search page. Start typing your term, then click “Show index” to the right of the search box.
Use the “Check index” button on the advanced search page to see if your phrase is included in PubMed’s Phrase index. From the National Library of Medicine.
For example, “Adult Non-Verbal Pain Scale” is not a phrase PubMed recognizes. Have PubMed look for the phrase with all words next to each other, in any order, by telling it to look in the title and abstract fields (tiab) with the words adjacent to each other (:~0):
Using proximity searching ([tiab:~0]) when a phrase is not included in PubMed’s phrase index can lead to more focused results compared to using quotation marks alone.
LibKey Nomad is a browser extension (available for Firefox, Chrome, Edge, Safari, and more!) that provides seamless one-click access to full-text MSK library resources from a wide variety of databases and journals!
Simply install the extension in your preferred browser; during installation you will be asked to select your organization – search and select Memorial Sloan Kettering Library.
How LibKey Nomad Works
Once you’ve downloaded and installed the LibKey Nomad browser extension, a new icon will appear at the bottom of the page when searching on various databases, websites, and journal platforms.
Note: Depending on the browser and/or the settings you have set, you may need to tell LibKey Nomad to allow access to a website, which you can usually set to always allow access to a specific site (eg. PubMed’s website). The browser extension should be visible in the top of your browser and will look like the green LibKey icon above.
Once the page loads, the browser extension will identify the citation(s) and, based on our library’s collection, will guide to access the full-text of each citation on the page.
If PDF full-text is available, a single-click Download PDF button will appear below the citation. If additional authentication is required you will be prompted to sign in via the MSK single sign-on. In most cases the PDF will be coming directly from the publisher or a supporting platform, however in some cases it may find the full-text through PubMed Central (PMC) or a institutional repository.
LibKey Nomad access buttons
Download PDF: In a single click the user should be able to either view the PDF in their browser or be prompted to download the PDF to their computer.
Article Link: Similar to the PDF full-text, this option appears when either the full-text is only available as HTML, or if a PDF is available but an additional click is required once arriving at the publisher’s website
Manuscript PDF: This option appears if the article has been located in a repository as an Accepted Manuscript; while this manuscript has been peer-reviewed and accepted for publication, it is likely not formatted for publication yet and may simply be a Word document converted to PDF
Manuscript Link: Like the Manuscript PDF button, this will appear if the manuscript is available, but not in PDF format (HTML, Word document, etc.)
Access Options: Lastly, if full-text cannot be located immediately, this button will bring you to the MSK Library catalog where you can submit a request through our document delivery service[
View Complete Issue [BrowZine]: Integration with BrowZine in certain databases will provide a link to the entire journal issue in BrowZine for a selected citation
Where can I use LibKey Nomad?
Third Iron is continually adding new platforms and publishers to their list of places with LibKey Nomad integration. Currently the extension is supported in a number of databases and websites, as well as a wide range of major journal and eBook publishers.
Note: These publisher sites and platforms represent the discovery starting points but do not represent the coverage of content which extends to*all* eBooks and journals within a libraries collection!
What’s the difference between libkey nomad and Browzine?
Both LibKey Nomad and BrowZine are produced by Third Iron and they work in conjunction to provide access electronic access to journal articles. LibKey Nomad is a browser extension to identify full-text articles on the web, while BrowZine is a platform to browse and read articles. In certain databases a citation may be able to provide both a link to download the PDF as well as a link to view the entire journal issue that the citation is found in.
