{"id":91,"date":"2013-08-22T22:41:59","date_gmt":"2013-08-22T22:41:59","guid":{"rendered":"http:\/\/evolvedmicrobe.com\/blogs\/?p=91"},"modified":"2013-08-23T14:44:21","modified_gmt":"2013-08-23T14:44:21","slug":"accessing-dbsnp-with-c-and-the-net-platform","status":"publish","type":"post","link":"http:\/\/evolvedmicrobe.com\/blogs\/?p=91","title":{"rendered":"Accessing dbSNP with C# and the .NET Platform"},"content":{"rendered":"

NCBI Entrez can be accessed with many different platforms (python, R, etc.) , but I find .NET one of the best because the static typing makes it easy to infer what all the datafields mean, and navigate the data with much greater ease. <\/p>

Documentation is sparse for this task, but here is how to access NCBI from the .NET platform.  The example steps\/program show how to query dbSNP for information about particular ids.<\/p>

  1. Open visual studio, start a new project and add two Service References to the project: <\/b>http:\/\/eutils.ncbi.nlm.nih.gov\/soap\/v2.0\/eutils.wsdl<\/b><\/a> and http:\/\/eutils.ncbi.nlm.nih.gov\/soap\/v2.0\/efetch_snp.wsdl<\/b><\/a> files. Note that the efetch depends on the database used, in this case \u201csnp\u201d other databases have different ones.  You should now have two references:\"image\"<\/a><\/li><\/ol>

    More information is available here on setting up visual studio: http:\/\/www.ncbi.nlm.nih.gov\/books\/NBK55694\/<\/a><\/p>

    2. Next up grab the data as shown in the example.  Each SNP has A LOT more data, which can be inspected in the IDE.<\/p> \r\n\r\n 

       1:  <\/span>static<\/span> void<\/span> Main(string<\/span>[] args)<\/pre>
       2:  <\/span>{        <\/pre>
       3:  <\/span>        string<\/span> dbSNPid=\"28357684\"<\/span>;<\/pre>
       4:  <\/span>        efetch.eFetchRequest re = new<\/span> efetch.eFetchRequest();<\/pre>
       5:  <\/span>        re.id = dbSNPid;<\/pre>
       6:  <\/span>        var serv=new<\/span> efetch.eUtilsServiceSoapClient();<\/pre>
       7:  <\/span>        var exchange = serv.run_eFetch(re);<\/pre>
       8:  <\/span>        var snpData = exchange.ExchangeSet.Rs[0];<\/pre>
       9:  <\/span>        object<\/span>[] dataToReport=new<\/span> object<\/span>[] {<\/pre>
      10:  <\/span>            snpData.Het.value<\/span>,<\/pre>
      11:  <\/span>            snpData.hgvs.First(),<\/pre>
      12:  <\/span>            snpData.PrimarySequence.First().accession,<\/pre>
      13:  <\/span>        };<\/pre>
      14:  <\/span>        Console.WriteLine( String.Join(\"\\t\"<\/span>,dataToReport.Select(x=>x.ToString()).ToArray())); <\/pre>
      15:  <\/span>        Console.ReadLine();<\/pre>
      16:  <\/span>}<\/pre><\/div>\r\n