Upload Search Results
Now that we have a protocol created, it’s time to run and upload all search results! This is the most involved portion of the application.
Results are either:
Automatically downloaded by us
Uploaded manually by you (uploading your search results file)
The Search Dashboard
Run Searches screen can be accessed from the Main Menu.
There are two ways to import search data:
Upload results files manually
Use the AutoSearch functionality.
Using Automated Searches
Automated searches are available for the following databases on different levels of consistency.
PubMed (Very Consistent)
PubMed Central (Very Consistent)
Cochrane Library (Medium)
Clinicalrials.gov (Medium)
FDA Maude Adverse Events (Medium)
Automated Search Protocol
Remember when you selected databases and thresholds like Max Result counts in the ‘Search Protocol’ section? These settings will be used when running the automated searches, so give them a double-check before continuing.
Run an Automated Search
It only takes one click to start your automated search. Click “RUn Auto Search” for the term you want to run.
Understanding Search Results and Status
The ‘State’ of a Search
There are 3 states a search can be in, indicated by background color of the row, and the Status Column
COMPLETE
Green
This search has been run and results imported successfully.
NOT RUN
Purple
The search is still pending, and needs to be run or uploaded.
ERROR
Red
The search experienced an error when processing.
Excluded
Orange
The search has been excluded (too many results, or 0).
Consider the five below searches. One is not run, two are excluded, one is complete, and one is an error.
Understanding the Search Result Counts
You will see 4 squares with different numbers relating to a specific Search’s results.
Expected
This is the number from the Search Terms page prediction. It is not always 100% accurate and doesn’t have to match the other fields.
Imported
This is the number of articles that were saved successfully into your CiteMed.io database.
Processed
This is the number of articles that were found in the search result file. This should match the ‘Imported’ count exactly.
Duplicates
These were the number of duplicate articles identified and marked during the search (we will search for duplicates across the entire project, not just a single search).
Running Manual Searches
What is a Manual Search?
Manual searches are when you go to a specific database to run the search yourself, and download the results for upload into CiteMed.io.
Why upload searches manually?
There are two reasons to do this yourself:
You want to use a database we don’t support automatic collection on (Like Embase)
The automatic download function is not working for you.
Which Databases Accept Manual Searches?
All databases except manual uploads. The following are required for manual upload:
Embase
How to Run Your Manual Searches
Instructions are provided in the application as well. But for specific examples and details of how to run, download, and upload a search you can find them here.
Perform the search and download the results file (see below document for Database Specific Instructions) Running Manual Searches on the CiteMed App
Click ‘Upload Manual Search’ for your specific search term and database. This is on the ‘Upload Search Results’ Page.
Upload the correct filetype , and click ‘Save’.
How to Perform The Right Manual Searches
Note that performing manual searches means you’re responsible for adding the right dates and article type filters to your search.
Additionally, you need to make sure that you are exporting those results into a file format we can read. In the above example, you can see for a PubMed search, XML, and TXT formats are accepted.
Accepted Database Export File Formats
PubMed
TXT, XML
PubMed Central
TXT, XML
ClinicalTrials.gov
CSV
Cochrane
TXT
Embase
RIS
FDA Maude
CSV
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