Extract Pubmed Affiliations

Extract the country names from Pubmed affiliations and visualize the extent of worldwide collaborations among researchers. For this, you need to have R and RStudio installed on your computer and an XML file created from Pubmed.

Creating and XML file form Pubmed

1. Go to Pubmed

2. Type the text in search bar and press Search button

3. In the results page, click Send to and then choose File and Format as XML. Click on Create File and choose the destination to save the XML file.

Working with R project

1. Open the PubmedAffiliationsProject folder and double click PubmedAffiliationsProject.Rproj file. It will open RStudio.

2. In the files pane of RStudio, click the script file PubmedAffiliations.R. Select entire script and press Run.

3. You will be asked for the location of XML file. Please select the location and press OK.

4. Once the extraction is done, you will be prompted that the output will be saved as output.csv in the PubmedAffiliationsProject folder.

5. Press OK and then open the output.csv file to see the results.

Note

• Work in progress to visualize the data in the form of maps.

• Please revisit the repository in few days.

Contributors

• Sunil Kumar Veeravalli veeravallisunil@gmail.com

Copyright

© Sunil Kumar Veeravalli