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How to efetch specific attributes from BioSamples?

I need to extract the sample source for a list of sample ids. I tried using efetch as follows:

efetch -db biosample -id SAMN04383980 -format xml | xtract -pattern BioSampleSet -division BioSample -group Attributes -element Attribute

The problem here is that there are often more than two attributes:

  <Attributes>
         <Attribute attribute_name="source_name" harmonized_name="source_name" display_name="source name">H7 hESCs</Attribute>
         <Attribute attribute_name="cell line" harmonized_name="cell_line" display_name="cell line">H7 derived</Attribute> 
  </Attributes>

How do I extract the one with attribute_name="source_name" only?

ncbi eutils xml
• 4,117 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Arindam Ghosh Arindam Ghosh

1 answer

using a xpath expression:

 wget -q -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=biosample&id=SAMN04383980" |\
   xmllint --xpath "/BioSampleSet/BioSample/Attributes/Attribute[@attribute_name='source_name']/text()"  -

H7 hESCs
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Any idea how to also export the attribute_name to have a nicely formatted table ?

• 0 views • link
written by fconstancias • fconstancias

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