从多级标记XML结构中提取数据

Question

I am trying to extract data from multi level structured XML file. The Input file will be

This is the search result of the query http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=24874852&retmode=xml&rettype=abstract&email=[e-mail]

Output of the query:

<?xml version="1.0" encoding="UTF-8"?>
<PubmedArticleSet>
    <PubmedArticle>
        <MedlineCitation Status="Publisher" Owner="NLM">
            <PMID Version="1">24874852</PMID>
            <DateCreated>
                <Year>2014</Year>
                <Month>5</Month>
                <Day>30</Day>
            </DateCreated>  
            <Article PubModel="Print-Electronic">
                <Journal> 
                    <ISSN IssnType="Electronic">1976-670X</ISSN>
                    <JournalIssue CitedMedium="Internet">
                        <PubDate>
                            <Year>2014</Year>
                            <Month>May</Month>
                            <Day>30</Day>
                        </PubDate>
                    </JournalIssue>
                    <Title>BMB reports</Title>
                    <ISOAbbreviation>BMB Rep</ISOAbbreviation>
                </Journal>
                <ArticleTitle>
                    Human selenium binding protein-1 (hSP56) is a negative regulator of HIF-1α and suppresses the malignant characteristics of prostate cancer cells.
                </ArticleTitle>
                <Pagination>
                    <MedlinePgn/>
                </Pagination>
                <ELocationID EIdType="pii">2831</ELocationID>
                <Abstract>
                    <AbstractText NlmCategory="UNLABELLED">
                        In the present study, we demonstrate that ectopic expression of 56-kDa human selenium binding protein-1 (hSP56) in PC-3 cells that do not normally express hSP56 results in a marked inhibition of cell growth in vitro and in vivo. Down-regulation of hSP56 in LNCaP cells that normally express hSP56 results in enhanced anchorage-independent growth. PC-3 cells expressing hSP56 exhibit a significant reduction of hypoxia inducible protein (HIF)-1α protein levels under hypoxic conditions without altering HIF-1α mRNA (HIF1A) levels. Taken together, our findings strongly suggest that hSP56 plays a critical role in prostate cells by mechanisms including negative regulation of HIF-1α, thus identifying hSP56 as a candidate anti-oncogene product.
                    </AbstractText>
                </Abstract>
                <AuthorList>
                    <Author>
                        <LastName>Jeong</LastName>
                        <ForeName>Jee-Yeong</ForeName>
                        <Initials>JY</Initials>
                        <Affiliation>
                            Laboratory for Cell and Molecular Biology, Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Department of Biochemistry and Cancer Research Institute, Kosin University College of Medicine, Busan, South Korea.
                        </Affiliation>
                    </Author>
                    <Author>
                        <LastName>Zhou</LastName>
                        <ForeName>Jin-Rong</ForeName>
                        <Initials>JR</Initials>
                    </Author>
                    <Author>
                        <LastName>Gao</LastName>
                        <ForeName>Chong</ForeName>
                        <Initials>C</Initials>
                    </Author>
                    <Author>
                        <LastName>Feldman</LastName>
                        <ForeName>Laurie</ForeName>
                        <Initials>L</Initials>
                    </Author>
                    <Author>
                        <LastName>Sytkowski</LastName>
                        <ForeName>Arthur J</ForeName>
                        <Initials>AJ</Initials>
                    </Author>
                </AuthorList>
                <Language>ENG</Language>
                <PublicationTypeList>
                    <PublicationType>JOURNAL ARTICLE</PublicationType>
                </PublicationTypeList>
                <ArticleDate DateType="Electronic">
                    <Year>2014</Year>
                    <Month>5</Month>
                    <Day>30</Day>
                </ArticleDate>
            </Article>
            <MedlineJournalInfo>
                <MedlineTA>BMB Rep</MedlineTA>
                <NlmUniqueID>101465334</NlmUniqueID>
                <ISSNLinking>1976-6696</ISSNLinking>
            </MedlineJournalInfo>
        </MedlineCitation>
        <PubmedData>
            <History>
                <PubMedPubDate PubStatus="entrez">
                    <Year>2014</Year>
                    <Month>5</Month>
                    <Day>31</Day>
                    <Hour>6</Hour>
                    <Minute>0</Minute>
                </PubMedPubDate>
                <PubMedPubDate PubStatus="pubmed">
                    <Year>2014</Year>
                    <Month>5</Month>
                    <Day>31</Day>
                    <Hour>6</Hour>
                    <Minute>0</Minute>
                </PubMedPubDate>
                <PubMedPubDate PubStatus="medline">
                    <Year>2014</Year>
                    <Month>5</Month>
                    <Day>31</Day>
                    <Hour>6</Hour>
                    <Minute>0</Minute>
                </PubMedPubDate>
            </History>
            <PublicationStatus>aheadofprint</PublicationStatus>
            <ArticleIdList>
                <ArticleId IdType="pii">2831</ArticleId>
                <ArticleId IdType="pubmed">24874852</ArticleId>
            </ArticleIdList>
        </PubmedData>
    </PubmedArticle>
</PubmedArticleSet>

My intention is to reorganise the data in another webpage. I am trying extract data from every layer of this structure. I am using regex. Eg, If I want to extract the abstract text from the xml structure, Here is the code I am using:

$o=urlencode("24874852");
$efetch = "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
db=pubmed&id=$o&retmode=xml&rettype=abstract&email=[e-mail]";
#echo $efetch;
$handle1 = file_get_contents($efetch,"r");
#echo $handle1s;
preg_match_all('/<AbstractText>\s*([0-9A-Za-z\.\_
]+)\s*   
<\/AbstractText>/s',$handle1,$abstext,PREG_PATTERN_ORDER)
foreach ($abstext[1] as $tiab){
echo $tiab; }`

I dont get the desired output that I expect. Any idea where it might have gone wrong?

Answer 1

If you are going to extract text from XML, the best option is to use an XML parser, such as a DOM parser:

$document = new DOMDocument(); 
$document->load( "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=24874852&retmode=xml&rettype=abstract&email=[e-mail]" ); 

From there you can use the XPath language to select the data you want to extract: //AbstractText will return a set of all <AbstractText> nodes.

You can use XPath in PHP on your parsed document:

$xpath = new DOMXpath($document);

To get all nodes you use:

$xpath->evaluate("//AbstractText")

And to extract the text from each node use nodeValue:

foreach ($xpath->evaluate("//AbstractText") as $abstractText) {
    echo $abstractText->nodeValue."
";
}

See a working example using your data here: http://codepad.viper-7.com/nlryKH