Question

Query hg37 rsid information

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2.7 years ago

Julian.dekker ▴ 20

Hi All,

I am trying to programmatically find information about hg19 rsids.

I tried to query ensemble but the information was on hg19, I also queried Kaviar (http://db.systemsbiology.net/kaviar/cgi-pub/Kaviar.pl). But in Kaviar I'm missing some rsids that I can find on other pages. I also looked at NCBI but it seems the information is on hg19 again.

Does anyone know an API to query for hg19 details? I need chromosome number and position.

Kind regards, Julian

hg37 rsid • 1.3k views

ADD COMMENT • link updated 2.7 years ago by manaswwm ▴ 550 • written 2.7 years ago by Julian.dekker ▴ 20

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Check out: https://www.ncbi.nlm.nih.gov/snp/

ADD REPLY • link 2.7 years ago by Pappu ★ 2.1k

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This could work but I find it difficult to process the API results for what I need, it should be possible just going to take me some work to filter all the unnecessary stuff out.

ADD REPLY • link 2.7 years ago by Julian.dekker ▴ 20

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FYI GRCh37 is hg19 not hg37 ;-)

ADD REPLY • link 2.7 years ago by Nicolas Rosewick 11k

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My bad sorry :D

ADD REPLY • link 2.7 years ago by Julian.dekker ▴ 20

score 2 · Accepted Answer · 2022-04-29

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2.7 years ago

manaswwm ▴ 550

I think Ensembl already has a REST-API dedicated for GRCh37 that you can find here - https://grch37.rest.ensembl.org/. For your case, I imagine this would be useful - https://grch37.rest.ensembl.org/documentation/info/variation_id

ADD COMMENT • link 2.7 years ago by manaswwm ▴ 550

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Thanks, This might be easiest since I already have code ready for the ensemble API.

ADD REPLY • link 2.7 years ago by Julian.dekker ▴ 20