Parsing PubMed XML using VB

Question

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SQL

Dim oNode As IXMLDOMNode

    For Each oNode In oItemNodes
        Set sPMIDNode = oNode.selectSingleNode("//PMID")
        If Not sPMIDNode Is Nothing Then sPMID = sPMIDNode.Text
        Set sTitleNode = oNode.selectSingleNode("//ArticleTitle")
        If Not STitleNode Is Nothing Then sTitle = STitleNode.Text
        Set SAbstractNode = oNode.selectSingleNode("//AbstractText")
        If Not SAbstractNode Is Nothing Then sAbstract = SAbstractNode.Text
    Next

I am having trouble getting the PMID, Article Title, and Abstract Text to line up correctly in a table when there is missing data. I have resorted to the following code, but I just get the first item in the node list repeated. How can I loop through the node list and get text values when they exist and have everything line up in the resulting table?

The XML from PubMed sometimes has an abstract and sometimes it does not. The oItemNodes is a node list of PubMed Articles. oNode increments correctly. SelectSingleNode does not work. It just finds the first Article.

Posted 26-Sep-12 13:03pm

tbarrus

Updated 26-Sep-12 16:36pm

v2

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Comments

Sergey Alexandrovich Kryukov 26-Sep-12 19:38pm

What do you mean by "VB"? (And, if this is something like VB6, better don't parse anything. :-)
--SA

tbarrus 26-Sep-12 22:30pm

Something like VB6. A DOM nodelist should work.

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Kuthuparakkal · Accepted Answer · 2012-09-26T15:22:00

Solution 1

try:

SQL

Dim oNode As IXMLDOMNode

    For Each oNode In oItemNodes
        Set sPMIDNode = oNode.selectSingleNode("/PMID")
        If Not sPMIDNode Is Nothing Then sPMID = sPMIDNode.Text
        Set sTitleNode = oNode.selectSingleNode("/ArticleTitle")
        If Not STitleNode Is Nothing Then sTitle = STitleNode.Text
        Set SAbstractNode = oNode.selectSingleNode("/AbstractText")
        If Not SAbstractNode Is Nothing Then sAbstract = SAbstractNode.Text
    Next

ref: http://msdn.microsoft.com/en-us/library/windows/desktop/ms757846(v=vs.85).aspx[^]

Posted 26-Sep-12 15:22pm

Kuthuparakkal

Comments

tbarrus 26-Sep-12 23:03pm

/PMID does not work because it is not a root node. PMID, ArticleTitle, and AbstractText are childnodes of PubMedArticle. Here are the exact XPath for each item:

/PubMedArticle/MedlineCitation/PMID

/PubMedArticle/MedlineCitation/PMID/Article/ArticleTitle

/PubMedArticle/MedlineCitation/PMID/Article/Abstract/AbstractText

Kuthuparakkal 27-Sep-12 0:34am

try
./PPMD

tbarrus 27-Sep-12 11:54am

Thanks for the hint. This worked (./MedlineCitation/PMID)