How to efetch specific attributes from BioSamples?

Question

[Arindam Ghosh]

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?

Answer 1

[Pierre Lindenbaum]

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

[fconstancias]

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