I'm having a relatively baffling problem - I'm trying to access the info for a bunch of BioSample IDs via the Entrez API in Python using Biopython v1.68, here's a minimal example. I'm looking for BioSample SAMEA2467098, URL: https://www.ncbi.nlm.nih.gov/biosample/?term=SAMEA2467098
This should be Brassica napus, cv. Beluga
In Python:
from Bio import Entrez
Entrez.email = 'SNIP'
sample = 'SAMEA2467098'
handle = Entrez.efetch('BioSample', id=sample, retmode='text')
print(handle.readlines())
['1: Non-tumor DNA sample from blood of a human participant in the dbGaP study "An APOBEC Cytidine Deaminase Mutagenesis in Human Cancers"\n', 'Identifiers: BioSample: SAMN02467098\n', 'Organism: Homo sapiens\n', 'Attributes:\n', ' /submitter handle="NHGRI_APOBEC_CytidineDeaminase"\n', ' /biospecimen repository="NHGRI_APOBEC_CytidineDeaminase"\n', ' /study name="An APOBEC Cytidine Deaminase Mutagenesis in Human Cancers"\n', ' /study design="Cross-Sectional"\n', ' /biospecimen repository sample id="TCGA-BP-5199-11A-01D-1429-08"\n', ' /submitted sample id="TCGA-BP-5199-11A-01D-1429-08"\n', ' /submitted subject id="TCGA-BP-5199-11A-01D-1429-08"\n', ' /study disease="Neoplasms"\n', ' /tissue="blood"\n', ' /analyte type="DNA"\n', ' /is tumor="No"\n', ' /subject is affected="Yes"\n', ' /molecular data type="SNV (.MAF)"\n', 'Accession: SAMN02467098\tID: 2467098\n', '\n', '\n']
Suddenly it's human, and the accession changed from SAME A 2467098 to SAM N0 2467098, which is indeed human: https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN02467098
What am I doing wrong here? It works for most of my other BioSample IDs!
Edit: It's not a Biopython problem, using the API manually gives the same result: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=biosample&id=SAMEA2467098&retmode=text
•
written
by
Philipp Bayer
2 answers
Hm, I think this has to do with the way Entrez handles IDs, if I use esearch first to get the BioSample's ID number it works:
This works, using esearch first:
handle = Entrez.esearch('BioSample', term='SAMEA2467098', id='text')
record = Entrez.read(handle)
record
{u'Count': '1', u'RetMax': '1', u'IdList': ['3769633'], u'TranslationStack': [{u'Count': '1', u'Field': 'All Fields', u'Term': 'SAMEA2467098[All Fields]', u'Explode': 'N'}, 'GROUP'], u'TranslationSet': [], u'RetStart': '0', u'QueryTranslation': 'SAMEA2467098[All Fields]'}
Using the new ID now in efetch:
handle = Entrez.efetch('BioSample', id=3769633, retmode='text')
handle.readlines()
['1: Beluga_PBY013; Beluga\n', 'Identifiers: BioSample: SAMEA2467098; SRA: ERS436855\n', 'Organism: Brassica napus\n', 'Attributes:\n', ' /sample name="ERS436855"\n', 'Accession: SAMEA2467098\tID: 3769633\n', '\n', '\n']
We're back at Beluga! But I'm still not 100% sure why this works the way it does, possibly the ID I'm entering clashes with the human entry or gets shortened for search.
Interesting, I can confirm this! I reckon because this one asks or a 'query' while I'm supplying an 'ID' above?
Yes, I think you're right because if I supply ID then efetch returns the human results.
efetch -db biosample -id "SAMEA2467098"
1: Non-tumor DNA sample from blood of a human participant in the dbGaP study "An APOBEC Cytidine Deaminase Mutagenesis in Human Cancers" Identifiers: BioSample: SAMN02467098 Organism: Homo sapiens
Two things,
NCBI Education Group has been offering webinars on this lately.
Check out some of the recent ones at:
https://www.ncbi.nlm.nih.gov/home/coursesandwebinars.shtml
Also, if you put in an issue here, we'll try to help you with a solution:
https://github.com/NCBI-Hackathons/EDirect_EUtils_API_Cookbook
Log in to answer this question.
May be worth creating a ticket at NCBI support. Looks like some sort of a bug in their code.
I dropped them a message late last night, looks like they'll file it as a bug, will update here
Any update on this issue ?
The bug doesn't seem to be fixed yet.
I haven't heard back anything, but just going over the middle step of using the returned ID works