This is a test version of Biostars. For the public version, visit https://www.biostars.org.
GIS overlay for environmental samples from NCBI

Hi all,

I was wondering if anyone is aware of an overlay for GIS GUI software (like ArcPro) showing where environmental samples (for NGS) were collected along with some basic metadata, like type of sequencing, library prep, etc. TIA!

ncbi environmental sra gis arcpro
• 839 views • link
written by noodle noodle

1 answer

If you setup one of the cloud-based SQL-like metadata search options, you can use the below code (for AWS-Athena) to find coordinates of samples, and then port over to whatever GIS system. Note that many samples will not have this information, or the information is only partial. There will be a bit of data-wrangling to still do after you retrieve this

https://www.ncbi.nlm.nih.gov/sra/docs/sra-bigquery/

https://www.ncbi.nlm.nih.gov/sra/docs/sra-bigquery-examples/

https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud-based-metadata-table/

SELECT
    element.k AS key,
    element.v AS value,
    *
FROM
    metadata,
    UNNEST("attributes") AS unnested(element)
WHERE
    element.k = 'lat_lon_sam_s_dpl34' AND
    REGEXP_LIKE(element.v, '[0-9]')
• 0 views • link
written by noodle noodle

Log in to answer this question.

More posts like this