Question: Some SNP XML document not available via an eutils query
0
gravatar for longoka
20 months ago by
longoka30
Cambridge/MA
longoka30 wrote:

Why are some XML documents available using a SNP query, and others are not?

For the first time today, I came across a SNP eutils search that did not return an XML:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=13422&report=XML

Whereas other searches return XMLs just fine:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=3000&report=XML

eutils snp xml • 488 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by longoka30

' looks like a bug

ADD REPLYlink written 20 months ago by Pierre Lindenbaum124k

I submitted a bug report to NCBI; I'll update this post when I get an answer.

FYI, I also tried executing this in R using the 'rentrez' package and the function 'entrez_fetch'; perhaps unsurprisingly, same result (see below).

entrez_fetch(db="snp", id = 13422, web_history = NULL, rettype = "FASTA", retmode = "XML",parsed = FALSE, config = NULL)

[1] "\n<ExchangeSet xmlns:xsi="\"&lt;a" href="https://www.w3.org/2001/XMLSchema-instance" rel="nofollow">https://www.w3.org/2001/XMLSchema-instance\" xmlns=\"https://www.ncbi.nlm.nih.gov/SNP/docsum\" xsi:schemaLocation=\"https://www.ncbi.nlm.nih.gov/SNP/docsum ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_eutils.xsd\" >\n</ExchangeSet>"
ADD REPLYlink modified 20 months ago • written 20 months ago by longoka30
1

The reply from the NBCI help esk:

Thanks for reporting this to us.

I did reproduce this, but I am not quite sure the underlying cost. Given that the SNP database is in a transitioning phase (both in workflow and web presentation), I am not quite sure how the API support through EUtils is to be carried over. I will need to get some clarification from the group.

You can take a look at the new web presentation and the API link there to see the API provided json blobs: https://www.ncbi.nlm.nih.gov/snp/rs13422

You can use the Feedback button to provide your comments/input to the group directly.

ADD REPLYlink modified 20 months ago • written 20 months ago by longoka30
0
gravatar for longoka
20 months ago by
longoka30
Cambridge/MA
longoka30 wrote:

I did not notice previously the 'API' link in the new dbSNP view:

https://www.ncbi.nlm.nih.gov/snp/rs13422

When you click on this link, it give the new API form:

https://api.ncbi.nlm.nih.gov/variation/v0/beta/refsnp/13422

This returns information on the SNP as a JSON blob.

It is unclear to me if it is a long-term plan for dbSNP to transition-away from making its data accessible via efetch and eutils, but they are supplying this alternative API, and it's quite nice.

ADD COMMENTlink written 20 months ago by longoka30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 731 users visited in the last hour