Getting taxonomy information from NCBI

Sometimes you need to get taxonomy information from NCBI, assuming that you know a particular species name. If you only are working with one species, then this is not very hard. When it comes to working with multiple species, however, attempting such a task using the web-frontend would be painful. Luckily, you can use the NCBI eutils to make the process somewhat easier, particularly when combined with BioPython:

Several things to remember here:

  • you must add your email address as the Entrez.email attribute

  • you should not request info. for more than 100 species during the work-day (see eutils restrictions)

  • you will need to make changes to get this to work with your particular input


comments powered by Disqus