Downloading BioSample records

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2.7 years ago

Valentin ▴ 10

Hello, I would like to download multiple records from BioSample (i.e., metadata) by their identifiers. For some reason I can't figure out how to do it in the same way as I download the sequences themselves. How can I do it? Thank you!

Entrez BioSample • 1.0k views

ADD COMMENT • link updated 2.6 years ago by seidel 11k • written 2.7 years ago by Valentin ▴ 10

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Take a look at previous solutions such as: How to pull metadata from SRA based on BioSample ID. There are a lot of ways to query.

ADD REPLY • link 2.7 years ago by seidel 11k

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I am sorry, it does not work - some of the records do not have corresponding SRA, for example this one https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN12837280. Thank you!

ADD REPLY • link 2.6 years ago by Valentin ▴ 10

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They don't need anything in SRA. You can query the BioSample database:

efetch -db biosample -id SAMN12837280 -format xml | xtract -pattern Attribute -element Attribute@attribute_name Attribute
isolate S141_64_esom
collection_date 2018-03
depth   1599.49
env_broad_scale marine hydrothermal vent biome [ENVO:01000030]
env_local_scale marine hydrothermal vent [ENVO:01000122]
env_medium      deep-sea hydrothermal deposit
geo_loc_name    Pacific Ocean
lat_lon 34.86111866 S 179.0576651 E
sample_type     metagenomic assembly
derived_from    This BioSample is a metagenomic assembly obtained from the hydrothermal vent metagenome BioSample: SAMN12239309
metagenomic     1
environmental-sample    1
metagenome-source       hydrothermal vent metagenome
isolation-source        deep-sea hydrothermal deposit

ADD REPLY • link 2.6 years ago by seidel 11k

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