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Find species biosample entries on NCBI with attached antibiograms

Hello biostars community,

I was wondering if anyone could point me in the right direction for searching for antibiograms for a particular species on NCBI's biosamples?

An example page can be found here.

I've so far been unable to find a way to search specifically for entries containing antibiogram data and would appreciate all the help I can get. Bonus points if you can manage it through entrez direct tools (eutils).

Thank you!

ncbi eutils
• 2,052 views • link
updated by Asaf Asaf • written by Jenez Jenez

1 answer

Interesting question, this might be very useful. I managed to get the data for you example using:

esearch -db biosample -query SAMN01163409 | efetch -mode xml

then parsing the XML. You can get this XML for all the bacteria with -query "%Bacteria" and parse the resulting huge XML.

• 0 views • link
written by Asaf Asaf

That's certainly one way of doing it. Maybe we'll see some proper integration in the future. Thanks mate.

• 0 views • link
written by Jenez Jenez

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