Question: question about API for SNPs
0
gravatar for ahm3dhany
4.5 years ago by
ahm3dhany10
ahm3dhany10 wrote:

Is there any API that i can send to it the rsID (e.g. rs4988235) and the API respond with the position (i.e. chromosome number and position of the nucleotide) and the effect related to this rsID (e.g. for Rs4988235, CC: likely to be lactose intolerant as an adult. CT: likely to be able to digest milk as an adult. TT: can digest milk.)

phenotype genotype snp api • 1.6k views
ADD COMMENTlink modified 4.5 years ago by Denise CS5.1k • written 4.5 years ago by ahm3dhany10
2
gravatar for Denise CS
4.5 years ago by
Denise CS5.1k
UK, Hinxton, EMBL-EBI
Denise CS5.1k wrote:

Yes, there is the Ensembl REST APIs. Two endpoints I could think of to get the data you are after are GET variation/:species/:ID (mainly) and the GET vep/:species/id/:id, which gives the added value of the annotation of your variant by the VEP. Check a previous biostars post.

ADD COMMENTlink written 4.5 years ago by Denise CS5.1k
1

the main problem is there is no phenotype (e.g. for Rs4988235, CC: likely to be lactose intolerant as an adult. CT: likely to be able to digest milk as an adult. TT: can digest milk.)

I want an API that give me something like this: (the screenshot is from SNPedia) enter image description here

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by ahm3dhany10
1

If you know PERL, you can use the Variation API and get the phenotype annotations. If you know R, biomaRt would be a good way to get the phenotype info as well.

ADD REPLYlink written 4.5 years ago by Denise CS5.1k

thanks for this info on Ensemble Restful apis

ADD REPLYlink written 2.7 years ago by gsr9999120
0
gravatar for karl.stamm
4.5 years ago by
karl.stamm3.9k
United States
karl.stamm3.9k wrote:

The dbSNP database can be queried for location and chromosome by RS#. You can download the dbSNP annotation and run queries on it, or maybe find an online resource.

For phenotype, it's much harder to be certain. The ClinVar database is another you can download that has a lot of those annotations, but most SNPs will not have known function.

ADD COMMENTlink written 4.5 years ago by karl.stamm3.9k

the main problem is there is no phenotype (e.g. for Rs4988235, CC: likely to be lactose intolerant as an adult. CT: likely to be able to digest milk as an adult. TT: can digest milk.)

I want an API that give me something like this: (the screenshot is from SNPedia) enter image description here

ADD REPLYlink written 4.5 years ago by ahm3dhany10
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