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 How to Save PubMed search results as a comma-separated value (CSV) file and import them into a spreadsheet		  
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(1) Do the desired search in PubMed (https://www.ncbi.nlm.nih.gov/pubmed/).


(2) Open FLink (https://www.ncbi.nlm.nih.gov/Structure/flink/flink.cgi).


(3) Open the "Please choose a database to start" menu and select "PubMed"


(4) Select "Input from Entrez History" from the dialog box that allows you to select your desired input method

  • use the pull-down menu on that tab to view a list of your recent PubMed searches
  • select the PubMed query for which you'd like to download a CSV formatted search results file
  • press "Submit"

(5) FLink will now display your search results in a "PubMed" folder tab


(6) Select the "Download CSV" option and choose to "open" or "save" the file, as desired.
     The browser window will also display the URL at which your results can be retrieved.


(7) The columns in a CSV file will depend on the database you accessed through FLink.
     For PubMed, the columns will include:

  • UID (PMID)
  • Authors
  • PubDate(Year)
  • PubDate(Month)
  • Title of article
  • Summary (which includes the following information in a single cell: Authors, title, journal name, year, month (if applicable), volume, issue, pages)

Tips for importing the comma-separated value (CSV) file into a spreadsheet application

  • The CSV file saved by FLink is in Unicode (UTF-8) format. If you plan to import the file into a spreadsheet program, you might need to specify the Unicode (UTF-8) format during the import process.

  • For example, if you plan to import the file into Excel, follow the instructions at Tune Help (https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/), starting with step 4, in order to import Unicode properly.

  • Note: If the Unicode (UTF-8) format is not specified during the process of importing the CSV file into the spreadsheet program, certain ASCII characters such as the umlaut (ö), e-acute (é), etc. might not appear correctly.



   

Additional Comments:


As noted on the "About FLink" page, the tool's main purpose is to traverse from a group of records in a "source" database (e.g., Proteins) to a ranked list of associated records in a "destination" database (e.g., BioSystems). As part of its functionality, one feature it offers is the ability to download lists of records in CSV format. This feature is available for any Entrez database that is supported in the FLink tool. Because PubMed is one of FLink's supported databases, you can save PubMed search results as a CSV file, even if you don't eventually link to a "destination" database.


Note that an additional "frequency" column will appear in any CSV file that contains data from a FLink "destination" database. In the example above, the CSV file does not contain a "frequency" column because we used PubMed as the starting ("source") database.


However, if you started your FLink operation in another database, such as Entrez Gene, and then used the "LinkTo" function to retrieve associated PubMed records, PubMed would be the "destination" database. In that case, the resulting PubMed CSV file would contain a "frequency" column, and the value in that column would indicate how many of the gene records from your input list had links to each PubMed record in your output list.


  
 
 
Revised 27 September 2016