Warning: The NCBI web site requires JavaScript to function. more...

My NCBI   Sign in to NCBI   Sign Out
Contents
Table of Contents Page
Print View

NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

Entrez Programming Utilities Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.

Bookshelf ID: NBK55695

Using Entrez Utilities Web Service with Visual Basic and MS Visual Studio 2008

Last Update: November 10, 2010.

Entrez Utilities Web Service has been tested with:

  • Microsoft .NET Framework Version 3.5 SP1
  • Microsoft Visual Studio 2008 Version 9.0.30729.1 SP

Creating a Web Service Client Project

The following walkthrough describes how to create a Visual Basic project to access the NCBI Entrez Utilities Web Service using MS Visual Studio 2005.

To create Windows application:

1.

Press Ctrl+Shift+N or Select File menu, then New, and then click Project to open the New Project dialog.

2.

Select Visual C# in Project types list.

3.

Select Windows Forms Application in Templates list.

4.

Click OK to create a new project.

5.

Select View menu and then Toolbox to open a Toolbox window.

6.

From the Toolbox, drag a Textbox and a Button to the design surface of Form1. Set Textbox’ Multiline property to true.

7.

On the Project menu, click Add Service Reference.

8.

In the Address field of the Add Service Reference dialog, type the URL http://eutils.ncbi.nlm.nih.gov/soap/v2.0/eutils.wsdl or path to local file (for example, C:\SOAP\eUtils\v2.0\eutils.wsdl) if you downloaded eUtils WSDL/XSD files from our FTP site

9.

Click the Go button to retrieve information about the XML Web service.

10.

In the Namespace field type eUtils.

11.

Click OK. The new eUtils item will appear in Service References list in the Solution Explorer view.

12.

Double-click the button on Form1 to create an event-handling method for this button.

13.

In the Button1_Click method enter the following code:

' eInfo utility returns a list of available databases
Try
Dim serv As New eUtils.eUtilsServiceSoapClient
Dim req As New eUtils.eInfoRequest
Dim res As eUtils.eInfoResult
' call NCBI EInfo utility
res = serv.run_eInfo(req)
TextBox1.Text = ""
Dim i As Integer
For i = 0 To res.DbList.Items.Length – 1
TextBox1.Text += res.DbList.Items(i) + Chr(13) + Chr(10)
Next i

Catch eee As Exception
TextBox1.Text = eee.ToString()
End Try

14.

Build and run application.

Important: Currently, the default maximum length of the SOAP message is only 64Kb. C# application fails when Web Service response size exceeds this value. To increase the limit open app.config file located in the application’s root directory and change all maxReceivedMessageSize and maxBufferSize parameters to the same larger value, for example, 2000000.

NCBI Entrez Utilities Web Service API

Below is a list of available methods.

Click on parameter to get its description.

Click on method name to see the example of use.

Public Function run_eGquery( ByVal eGqueryRequest As eGQueryRequest) As Result

eGqueryRequest class properties:

Public Function run_eInfo(ByVal eInfoRequest As eInfoRequest) As eInfoResult

eInfoRequest class properties:

Public Function run_eLink(ByVal eLinkRequest As eLinkRequest) As eLinkResult

eLinkRequest class properties:

Public Function run_ePost(ByVal ePostRequest As ePostRequest) As ePostResult

ePostRequest class properties:

Public Function run_eSearch(ByVal eSearchRequest As eSearchRequest) As SearchResult

eSearchRequest class properties:

Public Function run_eSpell(ByVal eSpellRequest As eSpellRequest) As eSpellResult

eSpellRequest class properties:

Public Function run_eSummary(ByVal eSummaryRequest As eSummaryRequest) As SummaryResult

eSummaryRequest class properties:

Public Function run_eFetch(ByVal eFetchRequest As eFetchRequest) As eFetchResult

eFetchRequest class properties:

Properties available for Sequence databases:

Examples

Call ' search in multiple Entrez databases Try Dim serv As New eUtils.eUtilsServiceSoapClient Dim req As New eUtils.eGqueryRequest Dim res As eUtils.Result ' call NCBI EGQuery utility req.term = "mouse" res = serv.run_eGquery(req) ' results output TextBox1.Text = "Search term: " + res.Term + Chr(13) + Chr(10) TextBox1.Text += "Results: " + Chr(13) + Chr(10) Dim i As Integer For i = 0 To res.eGQueryResult.ResultItem.Length - 1 TextBox1.Text += " " + res.eGQueryResult.ResultItem(i).DbName + _ ": " + res.eGQueryResult.ResultItem(i).Count + Chr(13) + Chr(10) Next i Catch eee As Exception TextBox1.Text = eee.ToString() End Try EGQuery 







Call ' eInfo utility returns an PMC db info Try Dim serv As New eUtils.eUtilsServiceSoapClient Dim req As New eUtils.eInfoRequest Dim res As eUtils.eInfoResult ' call NCBI EInfo utility req.db = "pmc" res = serv.run_eInfo(req) TextBox1.Text = "" TextBox1.Text += "DbName: " + res.DbInfo.DbName + Chr(13) + Chr(10) TextBox1.Text += "Description: " + res.DbInfo.Description + Chr(13) + Chr(10) TextBox1.Text += "MenuName: " + res.DbInfo.MenuName + Chr(13) + Chr(10) Catch eee As Exception TextBox1.Text = eee.ToString() End Try EInfo










Call ' put Id list to history for later use Try Dim serv As New eUtils.eUtilsServiceSoapClient Dim req As New eUtils.ePostRequest Dim res As New eUtils.ePostResult ' call NCBI EPost utility req.db = "pubmed" req.id = "123,456,37281,983621" res = serv.run_ePost(req) ' results output TextBox1.Text = "WebEnv: " + res.WebEnv + Chr(13) + Chr(10) + "QueryKey: " + res.QueryKey Catch eee As Exception TextBox1.Text = eee.ToString() End Try EPost









Call ' search in PubMed Central for stem cells in free fulltext articles Try Dim serv As New eUtils.eUtilsServiceSoapClient Dim req As New eUtils.eSearchRequest Dim res As eUtils.eSearchResult ' call NCBI ESearch utility ' NOTE: search term should be URL encoded req.db = "pmc" req.term = "stem+cells+AND+free+fulltext[filter]" req.RetStart = 0 req.RetMax = 15 res = serv.run_eSearch(req) ' results output TextBox1.Text = "Original query: stem cells AND free fulltext[filter]" + Chr(13) + Chr(10) TextBox1.Text += "Found ids: " + res.Count + Chr(13) + Chr(10) TextBox1.Text += "First " + res.RetMax + " ids: " Dim i As Integer For i = 0 To res.IdList.Length - 1 TextBox1.Text += res.IdList(i) + " " Next i Catch eee As Exception TextBox1.Text = eee.ToString() End Try ESearch









Call ' retrieves spelling suggestions Try Dim serv As New eUtils.eUtilsServiceSoapClient Dim req As New eUtils.eSpellRequest Dim res As eUtils.eSpellResult ' call NCBI ESpell utility req.db = "pubmed" req.term = "mouss" res = serv.run_eSpell(req) ' results output TextBox1.Text = "Misspelled word: " + res.Query + Chr(13) + Chr(10) TextBox1.Text += "Corrected word: " + res.CorrectedQuery Catch eee As Exception TextBox1.Text = eee.ToString() End Try ESpell









Call ' retrieves document Summaries for ID list Try Dim serv As New eUtils.eUtilsServiceSoapClient Dim req As New eUtils.eSummaryRequest Dim res As eUtils.eSummaryResult ' call NCBI ESummary utility req.db = "nuccore" req.id = "28864546,28800981" res = serv.run_eSummary(req) ' results output TextBox1.Text = "" Dim i As Integer For i = 0 To res.DocSum.Length - 1 TextBox1.Text += "ID: " + res.DocSum(i).Id + Chr(13) + Chr(10) Dim k As Integer For k = 0 To res.DocSum(i).Item.Length - 1 If Not res.DocSum(i).Item(k).ItemContent Is Nothing Then TextBox1.Text += " " + res.DocSum(i).Item(k).Name + _ ": " + res.DocSum(i).Item(k).ItemContent + Chr(13) + Chr(10) End If Next k TextBox1.Text += "-----------------------" + Chr(13) + Chr(10) + Chr(13) + Chr(10) Next i Catch eee As Exception TextBox1.Text = eee.ToString() End Try ESummary









Call EFetch



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


Taxonomy database example:


' fetch a record from Taxonomy database
    Try
      Dim serv As New eFetchTaxon.eUtilsServiceSoapClient
      Dim req As New eFetchTaxon.eFetchRequest
      Dim res As eFetchTaxon.eFetchResult
      ' call NCBI EFetch utility
      req.id = "9685"
      res = serv.run_eFetch(req)
      ' results output
      TextBox1.Text = res.TaxaSet(0).ScientificName + ": " + _
                      res.TaxaSet(0).Division + " (" + _
                      res.TaxaSet(0).Rank + ")" + Chr(10)
    Catch eee As Exception
      TextBox1.Text = eee.ToString()
    End Try







Search, Link & Fetch example



Add two Service References to the project: http://eutils.ncbi.nlm.nih.gov/soap/v2.0/eutils.wsdl and http://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_seq.wsdl files.


Name them eUtils and eFetchSeq correspondingly.



Important: Increase all maxReceivedMessageSize and maxBufferSize parameters in app.config file to 2000000 before running the application.



Dim ids(1) As String
        Dim fetchIds As String
        ids(0) = ""
        fetchIds = ""


        ' STEP #1: search in PubMed for "cat"
        '
        Try
            Dim serv As New eUtils.eUtilsServiceSoapClient
            Dim req As New eUtils.eSearchRequest
            Dim res As eUtils.eSearchResult
            ' call NCBI ESearch utility
            ' NOTE: search term should be URL encoded
            req.db = "pubmed"
            req.sort = "PublicationDate"
            req.term = "cat+AND+pubmed_nuccore[sb]"
            req.RetMax = "5"
            res = serv.run_eSearch(req)
            ' store UIDs for use in ELink
            Dim i As Integer
            For i = 0 To res.IdList.Length - 1
                If i > 0 Then
                    ids(0) += ","
                End If
                ids(0) += res.IdList(i)
            Next i


            TextBox1.Text = "Search in PubMed for cat returned " + res.Count + " hits" + Chr(13) + Chr(10)
            TextBox1.Text += "Search links in nuccore for the first 5 UIDs: " + ids(0) + Chr(13) + Chr(10) + Chr(13) + Chr(10)


        Catch eee As Exception
            TextBox1.Text += eee.ToString()
        End Try


        ' STEP #2: get links in nucleotide database (nuccore)
        '
        Try
            Dim serv As New eUtils.eUtilsServiceSoapClient
            Dim req As New eUtils.eLinkRequest
            Dim res As eUtils.eLinkResult
            ' call NCBI ELink utility
            req.dbfrom = "pubmed"
            req.db = "nuccore"
            req.id = ids
            res = serv.run_eLink(req)
            ' read result and create a list of UIDs to fetch
            Dim i As Integer
            For i = 0 To res.LinkSet(0).LinkSetDb(0).Link.Length - 1
                If i > 0 Then
                    fetchIds += ","
                End If
                fetchIds += res.LinkSet(0).LinkSetDb(0).Link(i).Id.Value
            Next i


            TextBox1.Text += "ELink returned the following UIDs from nuccore: " + fetchIds + Chr(13) + Chr(10) + Chr(13) + Chr(10)
        Catch eee As Exception
            TextBox1.Text += eee.ToString()
        End Try


        ' STEP #3: fetch records from nuccore
        '
        Try
            Dim serv As New eFetchSeq.eUtilsServiceSoapClient
            Dim req As New eFetchSeq.eFetchRequest
            Dim res As eFetchSeq.eFetchResult
            ' call NCBI EFetch utility
            req.db = "nuccore"
            req.id = fetchIds
            res = serv.run_eFetch(req)


            ' results output
            Dim i As Integer
            For i = 0 To Math.Min(4, res.GBSet.GBSeq.Length - 1)
                TextBox1.Text += "Organism: " + res.GBSet.GBSeq(i).GBSeq_organism + Chr(13) + Chr(10)
                TextBox1.Text += "Locus: " + res.GBSet.GBSeq(i).GBSeq_locus + Chr(13) + Chr(10)
                TextBox1.Text += "Definition: " + res.GBSet.GBSeq(i).GBSeq_definition + Chr(13) + Chr(10)
                TextBox1.Text += "----------------------" + Chr(13) + Chr(10) + Chr(13) + Chr(10)
            Next i


        Catch eee As Exception
            TextBox1.Text += eee.ToString()
        End Try







Using WebEnv & QueryKey example



Add two Service References to the project: http://eutils.ncbi.nlm.nih.gov/soap/v2.0/eutils.wsdl and http://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_pubmed.wsdl files.


Name them eUtils and eFetchPubmed correspondingly.



Important: Increase all maxReceivedMessageSize and maxBufferSize parameters in app.config file to 2000000 before running the application.



Dim WebEnv As String
        Dim query_key As String
        WebEnv = ""
        query_key = ""


        ' STEP #1: search in PubMed for "cat"
        '
        Try
            Dim serv As New eUtils.eUtilsServiceSoapClient
            Dim req As New eUtils.eSearchRequest
            Dim res As eUtils.eSearchResult
            ' call NCBI ESearch utility
            ' NOTE: search term should be URL encoded
            req.db = "pubmed"
            req.usehistory = "y"
            req.term = "cat"
            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" + Chr(13) + Chr(10)
            TextBox1.Text += "WebEnv: " + WebEnv + Chr(13) + Chr(10)
            TextBox1.Text += "QueryKey: " + query_key + Chr(13) + Chr(10) + Chr(13) + Chr(10)


        Catch eee As Exception
            TextBox1.Text += eee.ToString()
        End Try


        'STEP #2: fetch 5 records from pubmed starting from record #10
        Try
            Dim serv As New eFetchPubmed.eUtilsServiceSoapClient
            Dim req As New eFetchPubmed.eFetchRequest
            Dim res As eFetchPubmed.eFetchResult
            ' call NCBI EFetch utility
            req.WebEnv = WebEnv
            req.query_key = query_key
            req.retstart = 10
            req.retmax = 5
            res = serv.run_eFetch(req)
            ' results output
            ' PubmedArticleSet array can include articles of PubmedArticleType and
            ' PubmedBookArticleType types. There should be separate display method
            ' for each article's type.
            Dim i As Integer
            For i = 0 To res.PubmedArticleSet.Length - 1
                Dim art As eFetchPubmed.PubmedArticleType
                Dim book As eFetchPubmed.PubmedBookArticleType
                art = Nothing
                book = Nothing
                If TypeOf (res.PubmedArticleSet(i)) Is eFetchPubmed.PubmedArticleType Then
                    art = res.PubmedArticleSet(i)
                Else
                    book = res.PubmedArticleSet(i)
                End If


                If Not art Is Nothing Then
                    TextBox1.Text += "Type: Pubmed Article" + Chr(13) + Chr(10)
                    TextBox1.Text += "Title: " + art.MedlineCitation.Article.ArticleTitle.Value + Chr(13) + Chr(10)
                    TextBox1.Text += "--------------------------" + Chr(13) + Chr(10) + Chr(13) + Chr(10)
                End If
                If Not book Is Nothing Then
                    TextBox1.Text += "Type: Pubmed Book Article" + Chr(13) + Chr(10)
                    TextBox1.Text += "Title: " + book.BookDocument.ArticleTitle.Value + Chr(13) + Chr(10)
                    TextBox1.Text += "--------------------------" + Chr(13) + Chr(10) + Chr(13) + Chr(10)
                End If


            Next i


        Catch eee As Exception
            TextBox1.Text = eee.ToString()
        End Try






















Contents






Table of Contents Page







Print View














Cover of Entrez Programming Utilities Help 





Entrez Programming Utilities Help [Internet].


Bethesda (MD): National Center for Biotechnology Information (US); 2010-.















Entrez Programming Utilities Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-. Using Entrez Utilities Web Service with Visual Basic and MS Visual Studio 2008. [Updated 2010 Nov 10].













Download



















In this Page



















Other titles in this collection



















Recent Activity










ClearTurn OffTurn On



Your browsing activity is empty.


Activity recording is turned off.


Turn recording back on

See more...
































statistics 



Text Only Options


Top of page








Text Only Options




 Open the original version of this page. 





Usablenet Assistive is a UsableNet product. Usablenet Assistive Main Page.