Hello everyone!
I would like to know if there is a way to get all the id's from BioSample. I already tried a link that i saw in another post that works for BioProject (https://www.ncbi.nlm.nih.gov/bioproject/browse/) but it doesn´t work for BioSample.
I also tried to download the summary of BioSample using this example from BioProject (ftp://ftp.ncbi.nlm.nih.gov/bioproject/summary.txt)
Also, can this be solved programmatically, i.e. using Eutils or EDirect?
What i really want to know is, simply, how many id's exist and how can i search for a list of them.
Thank you very much!
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pedrorvc •
using my tool XsltStream http://lindenb.github.io/jvarkit/XsltStream.html and the NCBI Biosample XML dump
May I ask you why you need a list of all samples? And just the id's without any other information? I don't understand what you want to accomplish.
However, if you have a problem with ncbi's biosamples, you can try EBI's Biosample database (It should be synchronized with the ncbi one as far as I know). In this post I link to the API and the documentation, you might find that useful!
Of course, you could also access the data via RDF/SPARQL but that is a whole different story.
Thank you very much for your explanation. I am trying to get the BioSample id's associated with some BioProjects and i just wanted to know how much records existed and a way to list them.
You could get this file and then grep for sample accession #.
Edit: For specific BioProject ID's
esearch -db bioproject -query "BioProj_ID" | elink -target biosample | efetch -format docsum | xtract -pattern DocumentSummary -block Accession -element Accession
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