Data Mining from my Genomic Coordinates

Question

[Paul]

Hi everybody,

lot of us faced problem when reporting variants need to check some of the variants in UCSC genome browser, NCBI, ClinVAr or Ensembl and many others databases and tools to collect about my variants as much information as possible. Of course there are tool to annotate my variants like VEP, Annovar, SeatleSeq...

Do you have any experiences to generate from my genomic coordinate some output with direct links to dbSNP, UCSC, Ensembl, ClinVar...and many others ?

Lets assume my input is in hg38:

chr2 47475313 47475313

and output could look like:

chr2 47475313 dbSNP Variation_Viewer UCSC Ensembl ClinVar

Thank you for sharing your codes, workflows and experiences.

[Paul]

Of course I do not want to direct link only to this databases - share your favorite one!!

Answer 1

[Kevin Blighe]

I think that you will have to create your own script/program to do this. However, if each of these websites has input forms into which you can post your genomic co-ordinates, then this may be the way to go:

You can download a webpage with cURL:

curl https://www.ncbi.nlm.nih.gov/projects/SNP/ > dbsnp.txt

Use formfind to identify input boxes, buttons, etc. on the webpage:

formfind < dbsnp.txt

Using information of form element IDs from formfind, post the data to the form and retrieve the result:

curl -d id="201305711" https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi

Or provide a direct link using the information you've got (pseudocode):

URLdbSNP = "https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=" + rsID
URLvariationViewer = "https://www.ncbi.nlm.nih.gov/variation/view/?q=" + rsID + "&filters=source%3Adbsnp&assm=GCF_000001405.33"
et cetera

[Paul]

Thank you Kevin for your sharing experience. I was thinking if I am only one person who faced this question :)

[Kevin Blighe]

No problem Paul! :)

Good luck with it