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强大的NCBI接口

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Using Entrez Utilities Web Service with C# and MS Visual Studio 2005

Updated: May 20, 2008

  • Creating a Web Service Client Project
  • NCBI Entrez Utilities Web Service API
  • Examples
    • Search, Link & Fetch example
    • Using WebEnv & QueryKey example

 

Entrez Utilities Web Service has been tested with:

  • Microsoft Windows XP Professional (Service Pack2)
  • Microsoft .NET Framework Version 2.0.50727
  • Microsoft Visual Studio 2005 Version 8.0.50727.42

 

NCBI Entrez Utilities Web Service using MS Visual Studio 2005.

To create Windows application:

  • Press Ctrl+Shift+N or Select File menu, then New, and then click Project to open the New Project dialog.
  • Select Visual C# in Project types list.
  • Select Windows Application in Templates list.
  • Click OK to create a new project.
  • Select View menu and then Toolbox to open a Toolbox window.
  • From the Toolbox, drag a Textbox and a Button to the design surface of Form1.
  • On the Project menu, click Add Web Reference.
  • In the URL field of the Add Web Reference dialog, type the URL http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl
  • Click the Go button to retrieve information about the XML Web service.
  • In the Web reference name field, rename the Web reference to eUtils.
  • Click Add Reference to add a Web reference for the target XML Web service.
  • Double-click the button on Form1 to create an event-handling method for this button.
  • In the button1_Click method enter the following code:

     

    // eInfo utility returns a list of available databases

    try

    {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI EInfo utility

      eUtils.eInfoResult res = serv.run_eInfo(new eUtils.eInfoRequest());

      // results output

      textBox1.Text = ""; 

      for(int i=0; i<res.DbList.Items.Length; i++) textBox1.Text += res.DbList.Items[i]+"\r\n";

    }

    catch (Exception eee)

    {

      textBox1.Text = eee.ToString();

    }

  • Build and run application.

    •  

    eutils_MS.wsdl file.

    Click on parameter to get its description.

    Click on method name to see the example of use.

    public Result run_eGquery(eGqueryRequest params)eGqueryRequest class properties:  - String term  - String tool  - String emailpublic eInfoResult run_eInfo(eInfoRequest params)eInfoRequest class properties:  - String db  - String tool  - String emailpublic eLinkResult run_eLink(eLinkRequest params)eLinkRequest class properties: - String db- String[] id- String reldate- String mindate- String maxdate- String datetype- String term- String dbfrom- String WebEnv- String query_key- String cmd- String tool- String emailpublic ePostResult run_ePost(ePostRequest params) ePostRequest class properties:  - String db  - String id  - String tool  - String emailpublic eSearchResult run_eSearch(eSearchRequest params)eSearchRequest class properties:  - String db  - String term  - String WebEnv  - String query_key  - String usehistory  - String tool  - String email  - String field  - String reldate  - String mindate  - String maxdate  - String datetype  - String retstart  - String retmax  - String rettype  - String sort public eSpellResult run_eSpell(eSpellRequest params) eSpellRequest class properties: - String db  - String term  - String tool  - String emailpublic eSummaryResult run_eSummary(eSummaryRequest params)eSummaryRequest class properties:  - String db  - String id  - String WebEnv  - String query_key  - String retstart  - String retmax  - String tool  - String emailpublic eFetchResult run_eFetch(eFetchRequest params)eFetchRequest class properties: - String db - String id - String WebEnv - String query_key - String tool - String email - String retstart - String retmax - String rettype燩roperties available for Sequence databases: - String rettype - String strand - String seq_start - String seq_stop - String complexity - String report

    EGQuery

     

     

    try

    {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI EGQuery utility

      eUtils.eGqueryRequest req = new eUtils.eGqueryRequest();

      req.term = "mouse";

      eUtils.Result res = serv.run_eGquery(req);

      // results output

      textBox1.Text = "Search term: " + res.Term + "\r\n";

      textBox1.Text += "Results: \r\n";

      for(int i=0; i<res.eGQueryResult.ResultItem.Length; i++)

      {

      textBox1.Text += "  " + res.eGQueryResult.ResultItem[i].DbName +

    ": " + res.eGQueryResult.ResultItem[i].Count + "\r\n";

      }

    }

    catch (Exception eee)

    {

      textBox1.Text = eee.ToString();

    }

     

    EInfo

     

     

    // eInfo utility returns an PMC db info

    try

    {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI EInfo utility

      eUtils.eInfoRequest req = new eUtils.eInfoRequest();

      req.db = "pmc";

      eUtils.eInfoResult res = serv.run_eInfo(req);

      // results output

      textBox1.Text = "DbName: " + res.DbInfo.DbName + "\r\n" +

      "Description: " + res.DbInfo.Description + "\r\n" +

      "MenuName: " + res.DbInfo.MenuName + "\r\n";

    }

    catch (Exception eee)

    {

      textBox1.Text = eee.ToString();

    } 

     

    ELink

     

     

    // example retrieves links from Nuccore for to Protein GI 48819,7140345

    try

    {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      string[] id = {"48819,7140345"};

      // call NCBI ELink utility

      eUtils.eLinkRequest req = new eUtils.eLinkRequest();

      req.db = "protein";

      req.id = id;

      req.dbfrom = "nuccore";

      eUtils.eLinkResult res = serv.run_eLink(req);

      // results output

      textBox1.Text = "";

      for(int i=0; i<res.LinkSet.Length; i++)

      {

      textBox1.Text += "Links from " + res.LinkSet[i].DbFrom +

    " to " + res.LinkSet[i].LinkSetDb[0].DbTo + "\r\n";

      textBox1.Text += "  " + res.LinkSet[i].DbFrom + " id(s): ";

      for(int k=0; k<res.LinkSet[i].IdList.Length; k++)

      {

      textBox1.Text +=  res.LinkSet[i].IdList[k].Value + " ";

      }

      textBox1.Text += "\r\n";

      textBox1.Text += "  " + res.LinkSet[i].LinkSetDb[0].DbTo + " id(s): ";

      for(int k=0; k<res.LinkSet[i].LinkSetDb[0].Link.Length; k++)

      {

      textBox1.Text += res.LinkSet[i].LinkSetDb[0].Link[k].Id.Value + " ";

      }

      textBox1.Text += "\r\n----------------------\r\n";

      }

    }

    catch (Exception eee)

    {

      textBox1.Text = eee.ToString();

    } 

     

    EPost

     

     

    // Put ID list to history for later use

    try

    {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI ESpell utility

      eUtils.ePostRequest req = new eUtils.ePostRequest();

      req.db = "pubmed";

      req.id = "11237011";

      eUtils.ePostResult res = serv.run_ePost(req);

      // results output

      textBox1.Text = "WebEnv: "+res.WebEnv  + "\r\n";

      textBox1.Text += "QueryKey: "+res.QueryKey;

    }

    catch (Exception eee)

    {

      textBox1.Text = eee.ToString();

    } 

     

    ESearch

     

     

    // search in PubMed Central for stem cells in free fulltext articles

    try

    {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI ESearch utility

      // NOTE: search term should be URL encoded

      eUtils.eSearchRequest req = new eUtils.eSearchRequest();

      req.db = "pmc";

      req.sort = "SortDate";

      req.term = "stem+cells+AND+free+fulltext[filter]";

      req.RetStart = "0";

      req.RetMax = "15";

      eUtils.eSearchResult res = serv.run_eSearch(req);

      // results output

      textBox1.Text = "Original query: stem cells AND free fulltext[filter]\r\n";

      textBox1.Text += "Found ids: " + res.Count+"\r\n";

      textBox1.Text += "First " + res.RetMax +" ids: ";

     

      for(int i=0; i<res.IdList.Length; i++)

      {

      textBox1.Text += res.IdList[i] + " ";

      }

    }

    catch (Exception eee)

    {

      textBox1.Text = eee.ToString();

    }

     

    ESpell

     

     

    // retrieves spelling suggestions

    try

    {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI ESpell utility

      eUtils.eSpellRequest req = new eUtils.eSpellRequest();

      req.db = "pubmed";

      req.term = "mouss";

      eUtils.eSpellResult res = serv.run_eSpell(req);

      // results output

      textBox1.Text = "Misspelled word: "+res.Query + "\r\n";

      textBox1.Text += "Corrected word: "+res.CorrectedQuery;

    }

    catch (Exception eee)

    {

      textBox1.Text = eee.ToString();

    }

     

    ESummary

     

     

    // retreives document Summaries by list of primary IDs

    try

    {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI ESummary utility

      eUtils.eSummaryRequest req = new eUtils.eSummaryRequest();

      req.db = "nlmcatalog";

      req.id = "905";

      eUtils.eSummaryResult res = serv.run_eSummary(req);

      // results output

      textBox1.Text = "";

      for(int i=0; i<res.DocSum.Length; i++)

      {

      textBox1.Text += "ID: "+res.DocSum[i].Id+"\r\n";

      for(int k=0; k<res.DocSum[i].Items.Length; k++)

      {

      textBox1.Text += "  "+res.DocSum[i].Items[k].Name +": "+res.DocSum[i].Items[k].ItemContent + "\r\n";

      }

      textBox1.Text += "-----------------------\r\n\r\n";

      }

    }

    catch (Exception eee)

    {

      textBox1.Text = eee.ToString();

    }

     

    EFetch

    To fetch data from one of the supported databases add the corresponding Web Reference to project. For example, for taxonomy database in Add Web Reference dialog type http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_taxon.wsdl in URL field and eFetchTaxon in Web Reference Name.

    Taxonomy database example:

     

    // fetch a record from Taxonomy database

    try

    {

      eFetchTaxon.eFetchTaxonService serv = new eFetchTaxon.eFetchTaxonService();

      // call NCBI EFetch utility

      eFetchTaxon.eFetchRequest req = new eFetchTaxon.eFetchRequest();

      req.id = "9685";

      eFetchTaxon.eFetchResult res = serv.run_eFetch(req);

      // results output

      textBox1.Text = res.TaxaSet[0].ScientificName + ": " +

      res.TaxaSet[0].Division + " (" +

      res.TaxaSet[0].Rank + ")\r\n";

    }

    catch (Exception eee)

    {

      textBox1.Text = eee.ToString();

    }

     

     

    Search, Link & Fetch example

    Add two Web References to project for http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl and http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_seq.wsdl files. Name them eUtils and eFetchSeq correspondingly.

     

     

      String[] ids = { "" };

      String fetchIds = "";

     

      // STEP #1: search in PubMed for "cat"

      //

      try

      {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI ESearch utility

      // NOTE: search term should be URL encoded

      eUtils.eSearchRequest req = new eUtils.eSearchRequest();

      req.db = "pubmed";

      req.sort = "PublicationDate";

      req.term = "cat+AND+pubmed_nuccore[sb]";

      req.RetMax = "5";

      eUtils.eSearchResult res = serv.run_eSearch(req);

     

      // store UIDs for use in ELink

      int N = res.IdList.Length;

      for (int i = 0; i < N; i++)

      {

      if (i > 0) ids[0] += ",";

      ids[0] += res.IdList[i];

      }

      textBox1.Text = "Search in PubMed for \"cat\" returned " + res.Count + " hits\r\n";

      textBox1.Text += "Search links in nuccore for the first 5 UIDs: " + ids[0]+"\r\n\r\n";

     

      }

      catch (Exception eee)

      {

      textBox1.Text += eee.ToString();

      }

     

      // STEP #2: get links in nucleotide database (nuccore)

      try

      {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI ELink utility

      eUtils.eLinkRequest req = new eUtils.eLinkRequest();

      req.db = "nuccore";

      req.id = ids;

      req.dbfrom = "pubmed";

      eUtils.eLinkResult res = serv.run_eLink(req);

      // read result and create a list of UIDs to fetch

      for (int i = 0; i < res.LinkSet[0].LinkSetDb[0].Link.Length; i++)

      {

      if (i > 0) fetchIds += ",";

      fetchIds += res.LinkSet[0].LinkSetDb[0].Link[i].Id.Value;

    爙

      textBox1.Text += "ELink returned the following UIDs from nuccore: " + fetchIds + "\r\n\r\n";

      }

      catch (Exception eee)

      {

      textBox1.Text += eee.ToString();

      }

     

      // STEP #3: fetch records from nuccore

      //

      try

      {

      eFetchSeq.eFetchSequenceService serv = new eFetchSeq.eFetchSequenceService();

      // call NCBI ESpell utility

      eFetchSeq.eFetchRequest req = new eFetchSeq.eFetchRequest();

      req.db = "nuccore";

      req.id = fetchIds;

      eFetchSeq.eFetchResult res = serv.run_eFetch(req);

      // results output

      for (int i = 0; i < res.GBSet.GBSeq.Length; i++)

      {

      textBox1.Text += "Organism: " + res.GBSet.GBSeq[i].GBSeq_organism + "\r\n";

      textBox1.Text += "Locus: " + res.GBSet.GBSeq[i].GBSeq_locus + "\r\n";

      textBox1.Text += "Definition: " + res.GBSet.GBSeq[i].GBSeq_definition + "\r\n";

      textBox1.Text += "----------------------\r\n\r\n";

      }

      }

      catch (Exception eee)

      {

      textBox1.Text += eee.ToString();

      }

     

     Using WebEnv & QueryKey example

    Add two Web References to project for http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl and http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_pubmed.wsdl files. Name them eUtils and eFetchPubmed correspondingly.

     

      String WebEnv = "";

      String query_key = "";

     

      // STEP #1: search in PubMed for "cat"

     //

      try

      {

      eUtils.eUtilsService serv = new eUtils.eUtilsService();

      // call NCBI ESearch utility

      // NOTE: search term should be URL encoded

      eUtils.eSearchRequest req = new eUtils.eSearchRequest();

      req.db = "pubmed";

      req.term = "cat";

      req.usehistory = "y";

      eUtils.eSearchResult res = serv.run_eSearch(req);

      // store WebEnv & QueryKey for use in eFetch

      WebEnv = res.WebEnv;

      query_key = res.QueryKey;

     

      textBox1.Text = "Search in PubMed for \"cat\" returned " + res.Count + " hits\r\n";

      textBox1.Text += "WebEnv: " + WebEnv + "\r\n";

      textBox1.Text += "QueryKey: " + query_key + "\r\n\r\n";

     

      }

      catch (Exception eee)

      {

      textBox1.Text += eee.ToString();

      }

     

      // STEP #2: fetch 5 records from pubmed starting from record #10

      //

      try

      {

      eFetchPubmed.eFetchPubmedService serv = new eFetchPubmed.eFetchPubmedService();

      // call NCBI EFetch utility

      eFetchPubmed.eFetchRequest req = new eFetchPubmed.eFetchRequest();

      req.WebEnv = WebEnv;

      req.query_key = query_key;

      req.retstart = "10";

      req.retmax = "5";

      eFetchPubmed.eFetchResult res = serv.run_eFetch(req);

      // results output

      for (int i = 0; i < res.PubmedArticleSet.Length; i++)

      {

      textBox1.Text += "Title: " + res.PubmedArticleSet[i].MedlineCitation.Article.ArticleTitle + "\r\n";

      textBox1.Text += "Abstract: " + res.PubmedArticleSet[i].MedlineCitation.Article.Abstract.AbstractText + "\r\n";

      textBox1.Text += "--------------------------\r\n\r\n";

      }

      }

      catch (Exception eee)

      {

      textBox1.Text += eee.ToString();

      }

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