FLink!

FLinkDid you ever want to save PubMed search results in a format that would easily allow you to import them into an Excel spreadsheet?

NCBI to the rescue, once again, with FLink!

FLink (short for “frequency-weighted links”) can help you save PubMed search results as a CSV (comma-separated value) formatted file. The main purpose of FLink is actually 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 – which you can then import into Excel. This feature is available for any Entrez database that is supported in the FLink tool (see Supported Databases for a list). 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.  If that sounds like it might be helpful, please feel free to give FLink a try.

Here’s how to save PubMed results as a CSV formatted file using FLink:

1. Enter the desired query in PubMed

2. Open FLink (http://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. Simply use the pull-down menu and select the query you’d like to download.

5. FLink will now display your search results in a PubMed folder tab.

6. Select “Download CSV”. Now you can choose to save or open the file.

FLink does more than this, however. See the FLink overview for additional information.

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