GIS overlay for environmental samples from NCBI

Question

[noodle]

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!

Answer 1

[noodle]

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]')