How to extract Isolation source Attributes from Biosample db using NCBI eutils
Hello,
I am trying extract Isolation source attributes from ncbi Biosample database using ncbi eutils. I used following command but it's not returning empty
esearch -db biosample -query "SAMN02850961" | efetch -format xml | xtract -pattern BioSampleSet -element Attributes display_source
Please let me know what I am doing wrong.
Thanks in Advance.
1 answer
$ esearch -db biosample -query "SAMN02850961" | efetch -format xml | xtract -pattern BioSampleSet -element Attribute
DNF00037 missing missing HMP2129 Corynebacterium tuscaniense DNF00037 vagina Homo sapiens missing
or
$ esearch -db biosample -query "SAMN02850961" | efetch -format native | grep isolation
/isolation source="vagina"
Log in to answer this question.
More posts like this
-
How to pull metadata from SRA based on Run id?
written by Sidra •
-
How to pull metadata from SRA based on Run id?
written by Sidra •
-
Getting family level from taxonomy via E-Utils for virus classification
written by AUROSHIS •
-
problem with retrieving multiple records from Entrez using while read loop
written by hans •
-
How can I find genomes that have linked transcriptome data ? (bacteria)
written by hugo.avila
-
Export ensembl efetch in comma-delimited format
written by marongiu.luigi
-
Extracting all information about a sample when using xtract from e-utilities
written by An Ignorant Wanderer •
-
Downloading assemblies with description from NCBI with edirect
written by agata •
-
How to efetch specific attributes from BioSamples?
written by Arindam Ghosh
-
Edirect utility xtract conditional error question
written by him1532 •
