Execute Literature Search

When the research question has been finalized, it's time to check the literature.

From the list on Nests, select your Nest.

The Nest menu is the left-side column of buttons. Click on “Literature Search”.

Click on the “Add Search” button.

From the drop-down, select the Search Engine or database you would like to set up automatic API-based search on. Nested Knowledge supports PubMed, EuropePMC, and ClinicalTrials.gov.

For any other search engine or database, you will need to import using File Import rather than running directly via API.

Each of these search engines use Boolean queries, so you can use AND, OR, NOT, and parentheses to connect different terms. For specific guidance on constructing queries, use the search-engine-specific-links here:

• PubMed
• EuropePMC
• ClinicalTrials.gov
• Directory of Open Access Journals (DOAJ)

Type your search terms into the “Query” box, type the same as you would in a search engine. Use parentheses and terms such as AND, OR, NOT, in between your phrases. Click HERE for tips on how to create a great literature search.

Below the “Query” box, there is a drop-down list of search engines you can choose from. You may add a date filter and choose to run the search only once or have it repeatedly run over time (ex: monthly, etc).

Once you've completed entering all terms, chosen the search engine and schedule of running the search. Click “Add” in the bottom right corner of the window.

Once you add the new search, it will run and be listed at the top of your searches. The added studies will be ready to be screened in the Nest menu. To view a list of the studies generated by each individual search, under “Details” menu, click “Results: ####”. You will be taken to Study Inspector with the list of generated records for that particular search.

To view details of a particular search after addition, select “More”. Here you can view the full query, add any notes, view when and how the search was executed, and turn on Notifications.

For recurring searches, you may wish to receive an email notification when the search is rerun to keep track of updates made. To do this select “More” on your listed search, select “Notifications” then you can choose to have the notifications sent to the nest owner or admin(s). Notifications will not be sent when the search is run manually.

If no specific nest owner or admins are assigned, i.e. when the organization owns the nest, they will be sent to the owner or admins of the organization.

When you have confirmed that your final search(es) represent all records you would like to review in your nest, proceed to Screening.

• Viewing Search History
  • To see the full term that was searched on the search engine and the dates on which it was searched, as well as the number of studies retrieved, you can hover over a study and click “Full History“.
• Deletion Warning
  • If you delete a search, you will delete all studies found through that search term, all screening, tagging, extraction data, and any live/updatable export from those studies. Do not delete a search unless you want to remove all results related to it.
• No Editing
  • To ensure a consistent search record, you cannot edit a search term once executed. You can delete it (see above warning) and replace it, but you cannot edit a search once it is added.