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PubMed XML.js
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{
"translatorID": "fcf41bed-0cbc-3704-85c7-8062a0068a7a",
"label": "PubMed XML",
"creator": "Simon Kornblith, Michael Berkowitz, Avram Lyon, and Rintze Zelle",
"target": "xml",
"minVersion": "2.1.9",
"maxVersion": "",
"priority": 100,
"configOptions": {
"dataMode": "xml/dom"
},
"inRepository": true,
"translatorType": 1,
"browserSupport": "gcsibv",
"lastUpdated": "2015-03-21 14:39:07"
}
/*******************************
* Import translator functions *
*******************************/
function detectImport() {
var text = Zotero.read(1000);
return text.indexOf("<PubmedArticleSet>") != -1;
}
function processAuthors(newItem, authorsLists) {
for(var j=0, m=authorsLists.length; j<m; j++) {
//default to 'author' unless it's 'editor'
var type = "author";
if(authorsLists[j].hasAttribute('Type')
&& authorsLists[j].getAttribute('Type') === "editors") {
type = "editor";
}
var authors = ZU.xpath(authorsLists[j], 'Author');
for(var k=0, l=authors.length; k<l; k++) {
var author = authors[k];
var lastName = ZU.xpathText(author, 'LastName');
var firstName = ZU.xpathText(author, 'FirstName');
if(!firstName) {
firstName = ZU.xpathText(author, 'ForeName');
}
var suffix = ZU.xpathText(author, 'Suffix');
if(suffix && firstName) {
firstName += ", " + suffix
}
if(firstName || lastName) {
var creator = ZU.cleanAuthor(lastName + ', ' + firstName, type, true);
if(creator.lastName.toUpperCase() == creator.lastName) {
creator.lastName = ZU.capitalizeTitle(creator.lastName, true);
}
if(creator.firstName.toUpperCase() == creator.firstName) {
creator.firstName = ZU.capitalizeTitle(creator.firstName, true);
}
newItem.creators.push(creator);
} else if(lastName = ZU.xpathText(author, 'CollectiveName')) {
//corporate author
newItem.creators.push({
creatorType: type,
lastName: lastName,
fieldMode: 1
});
}
}
}
}
function doImport() {
var doc = Zotero.getXML();
var pageRangeRE = /(\d+)-(\d+)/g;
//handle journal articles
var articles = ZU.xpath(doc, '/PubmedArticleSet/PubmedArticle');
for(var i=0, n=articles.length; i<n; i++) {
var newItem = new Zotero.Item("journalArticle");
var citation = ZU.xpath(articles[i], 'MedlineCitation')[0];
var article = ZU.xpath(citation, 'Article')[0];
var title = ZU.xpathText(article, 'ArticleTitle');
if(title) {
if(title.charAt(title.length-1) == ".") {
title = title.substring(0, title.length-1);
}
newItem.title = title;
}
var fullPageRange = ZU.xpathText(article, 'Pagination/MedlinePgn');
if(fullPageRange) {
//where page ranges are given in an abbreviated format, convert to full
pageRangeRE.lastIndex = 0;
var range;
while(range = pageRangeRE.exec(fullPageRange)) {
var pageRangeStart = range[1];
var pageRangeEnd = range[2];
var diff = pageRangeStart.length - pageRangeEnd.length;
if(diff > 0) {
pageRangeEnd = pageRangeStart.substring(0,diff) + pageRangeEnd;
var newRange = pageRangeStart + "-" + pageRangeEnd;
fullPageRange = fullPageRange.substring(0, range.index) //everything before current range
+ newRange //insert the new range
+ fullPageRange.substring(range.index + range[0].length); //everything after the old range
//adjust RE index
pageRangeRE.lastIndex += newRange.length - range[0].length;
}
}
newItem.pages = fullPageRange;
}
var journal = ZU.xpath(article, 'Journal')[0];
if(journal) {
newItem.ISSN = ZU.xpathText(journal, 'ISSN');
var abbreviation;
if((abbreviation = ZU.xpathText(journal, 'ISOAbbreviation'))) {
newItem.journalAbbreviation = abbreviation;
} else if((abbreviation = ZU.xpathText(journal, 'MedlineTA'))) {
newItem.journalAbbreviation = abbreviation;
}
var title = ZU.xpathText(journal, 'Title');
if(title) {
title = ZU.trimInternal(title);
// Fix sentence-cased titles, but be careful...
if(!( // of accronyms that could get messed up if we fix case
/\b[A-Z]{2}/.test(title) // this could mean that there's an accronym in the title
&& (title.toUpperCase() != title // the whole title isn't in upper case, so bail
|| !(/\s/.test(title))) // it's all in upper case and there's only one word, so we can't be sure
)) {
title = ZU.capitalizeTitle(title, true);
}
newItem.publicationTitle = title;
} else if(newItem.journalAbbreviation) {
newItem.publicationTitle = newItem.journalAbbreviation;
}
// (do we want this?)
if(newItem.publicationTitle) {
newItem.publicationTitle = ZU.capitalizeTitle(newItem.publicationTitle);
}
var journalIssue = ZU.xpath(journal, 'JournalIssue')[0];
if(journalIssue) {
newItem.volume = ZU.xpathText(journalIssue, 'Volume');
newItem.issue = ZU.xpathText(journalIssue, 'Issue');
var pubDate = ZU.xpath(journalIssue, 'PubDate')[0];
if(pubDate) { // try to get the date
var day = ZU.xpathText(pubDate, 'Day');
var month = ZU.xpathText(pubDate, 'Month');
var year = ZU.xpathText(pubDate, 'Year');
if(day) {
newItem.date = month+" "+day+", "+year;
} else if(month) {
newItem.date = month+" "+year;
} else if(year) {
newItem.date = year;
} else {
newItem.date = ZU.xpathText(pubDate, 'MedlineDate');
}
}
}
}
var authorLists = ZU.xpath(article, 'AuthorList');
processAuthors(newItem, authorLists);
newItem.language = ZU.xpathText(article, 'Language');
var keywords = ZU.xpath(citation, 'MeshHeadingList/MeshHeading');
for(var j=0, m=keywords.length; j<m; j++) {
newItem.tags.push(ZU.xpathText(keywords[j], 'DescriptorName'));
}
var abstractSections = ZU.xpath(article, 'Abstract/AbstractText');
var abstractNote = [];
for(var j=0, m=abstractSections.length; j<m; j++) {
var abstractSection = abstractSections[j];
var paragraph = abstractSection.textContent.trim();
if(paragraph) paragraph += '\n';
var label = abstractSection.hasAttribute("Label") && abstractSection.getAttribute("Label");
if(label && label != "UNLABELLED") {
paragraph = label + ": " + paragraph;
}
abstractNote.push(paragraph);
}
newItem.abstractNote = abstractNote.join('');
newItem.DOI = ZU.xpathText(articles[i], 'PubmedData/ArticleIdList/ArticleId[@IdType="doi"]');
var PMID = ZU.xpathText(citation, 'PMID');
var PMCID = ZU.xpathText(articles[i], 'PubmedData/ArticleIdList/ArticleId[@IdType="pmc"]');
if(PMID) {
newItem.extra = "PMID: "+PMID;
//this is a catalog, so we should store links as attachments
newItem.attachments.push({
title: "PubMed entry",
url: "http://www.ncbi.nlm.nih.gov/pubmed/" + PMID,
mimeType: "text/html",
snapshot: false
});
}
if (PMCID) {
newItem.extra = (newItem.extra ? newItem.extra + "\n" : "")
+ "PMCID: " + PMCID;
}
newItem.complete();
}
//handle books and chapters
var books = ZU.xpath(doc, '/PubmedArticleSet/PubmedBookArticle');
for(var i=0, n=books.length; i<n; i++) {
var citation = ZU.xpath(books[i], 'BookDocument')[0];
//check if this is a section
var sectionTitle = ZU.xpathText(citation, 'ArticleTitle');
var isBookSection = !!sectionTitle;
var newItem = new Zotero.Item(isBookSection ? 'bookSection' : 'book');
if(isBookSection) {
newItem.title = sectionTitle;
}
var book = ZU.xpath(citation, 'Book')[0];
//title
var title = ZU.xpathText(book, 'BookTitle');
if(title) {
if(title.charAt(title.length-1) == ".") {
title = title.substring(0, title.length-1);
}
if(isBookSection) {
newItem.publicationTitle = title;
} else {
newItem.title = title;
}
}
//date
//should only need year for books
newItem.date = ZU.xpathText(book, 'PubDate/Year');
//edition
newItem.edition = ZU.xpathText(book, 'Edition');
//series
newItem.series = ZU.xpathText(book, 'CollectionTitle');
//volume
newItem.volume = ZU.xpathText(book, 'Volume');
//place
newItem.place = ZU.xpathText(book, 'Publisher/PublisherLocation');
//publisher
newItem.publisher = ZU.xpathText(book, 'Publisher/PublisherName');
//chapter authors
if(isBookSection) {
var authorsLists = ZU.xpath(citation, 'AuthorList');
processAuthors(newItem, authorsLists);
}
//book creators
var authorsLists = ZU.xpath(book, 'AuthorList');
processAuthors(newItem, authorsLists);
//language
newItem.language = ZU.xpathText(citation, 'Language');
//abstractNote
newItem.abstractNote = ZU.xpathText(citation, 'Abstract/AbstractText');
//rights
newItem.rights = ZU.xpathText(citation, 'Abstract/CopyrightInformation');
//seriesNumber, numPages, numberOfVolumes
//not available
//ISBN
newItem.ISBN = ZU.xpathText(book, 'Isbn');
var PMID = ZU.xpathText(citation, 'PMID');
if(PMID) {
newItem.extra = "PMID: "+PMID;
//this is a catalog, so we should store links as attachments
newItem.attachments.push({
title: "PubMed entry",
url: "http://www.ncbi.nlm.nih.gov/pubmed/" + PMID,
mimeType: "text/html",
snapshot: false
});
}
newItem.callNumber = ZU.xpathText(citation,
'ArticleIdList/ArticleId[@IdType="bookaccession"]');
//attach link to the bookshelf page
if(newItem.callNumber) {
var url = "http://www.ncbi.nlm.nih.gov/books/" + newItem.callNumber + "/";
if(PMID) { //books with PMIDs appear to be hosted at NCBI
newItem.url = url;
//book sections have printable views, which can stand in for full text PDFs
if(newItem.itemType == 'bookSection') {
newItem.attachments.push({
title: "Printable HTML",
url: 'http://www.ncbi.nlm.nih.gov/books/'
+ newItem.callNumber + '/?report=printable',
mimeType: 'text/html',
snapshot: true
});
}
} else { //currently this should not trigger, since we only import books with PMIDs
newItem.attachments.push({
title: "NCBI Bookshelf entry",
url: "http://www.ncbi.nlm.nih.gov/books/" + newItem.callNumber + "/",
mimeType: "text/html",
snapshot: false
});
}
}
newItem.complete();
}
}
/** BEGIN TEST CASES **/
var testCases = [
{
"type": "import",
"input": "<?xml version=\"1.0\"?>\n<!DOCTYPE PubmedArticleSet PUBLIC \"-//NLM//DTD PubMedArticle, 1st January 2015//EN\" \"http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_150101.dtd\">\n<PubmedArticleSet>\n<PubmedArticle>\n <MedlineCitation Owner=\"NLM\" Status=\"MEDLINE\">\n <PMID Version=\"1\">20729678</PMID>\n <DateCreated>\n <Year>2010</Year>\n <Month>08</Month>\n <Day>23</Day>\n </DateCreated>\n <DateCompleted>\n <Year>2010</Year>\n <Month>12</Month>\n <Day>21</Day>\n </DateCompleted>\n <Article PubModel=\"Print\">\n <Journal>\n <ISSN IssnType=\"Electronic\">1538-9855</ISSN>\n <JournalIssue CitedMedium=\"Internet\">\n <Volume>35</Volume>\n <Issue>5</Issue>\n <PubDate>\n <MedlineDate>2010 Sep-Oct</MedlineDate>\n </PubDate>\n </JournalIssue>\n <Title>Nurse educator</Title>\n <ISOAbbreviation>Nurse Educ</ISOAbbreviation>\n </Journal>\n <ArticleTitle>Zotero: harnessing the power of a personal bibliographic manager.</ArticleTitle>\n <Pagination>\n <MedlinePgn>205-7</MedlinePgn>\n </Pagination>\n <ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1097/NNE.0b013e3181ed81e4</ELocationID>\n <Abstract>\n <AbstractText>Zotero is a powerful free personal bibliographic manager (PBM) for writers. Use of a PBM allows the writer to focus on content, rather than the tedious details of formatting citations and references. Zotero 2.0 (http://www.zotero.org) has new features including the ability to synchronize citations with the off-site Zotero server and the ability to collaborate and share with others. An overview on how to use the software and discussion about the strengths and limitations are included.</AbstractText>\n </Abstract>\n <AuthorList CompleteYN=\"Y\">\n <Author ValidYN=\"Y\">\n <LastName>Coar</LastName>\n <ForeName>Jaekea T</ForeName>\n <Initials>JT</Initials>\n <AffiliationInfo>\n <Affiliation>School of Nursing, Georgia College & State University, Milledgeville, Georgia 61061, USA.</Affiliation>\n </AffiliationInfo>\n </Author>\n <Author ValidYN=\"Y\">\n <LastName>Sewell</LastName>\n <ForeName>Jeanne P</ForeName>\n <Initials>JP</Initials>\n </Author>\n </AuthorList>\n <Language>eng</Language>\n <PublicationTypeList>\n <PublicationType UI=\"D016428\">Journal Article</PublicationType>\n </PublicationTypeList>\n </Article>\n <MedlineJournalInfo>\n <Country>United States</Country>\n <MedlineTA>Nurse Educ</MedlineTA>\n <NlmUniqueID>7701902</NlmUniqueID>\n <ISSNLinking>0363-3624</ISSNLinking>\n </MedlineJournalInfo>\n <CitationSubset>N</CitationSubset>\n <MeshHeadingList>\n <MeshHeading>\n <DescriptorName MajorTopicYN=\"Y\" UI=\"D001634\">Bibliography as Topic</DescriptorName>\n </MeshHeading>\n <MeshHeading>\n <DescriptorName MajorTopicYN=\"Y\" UI=\"D003628\">Database Management Systems</DescriptorName>\n </MeshHeading>\n <MeshHeading>\n <DescriptorName MajorTopicYN=\"N\" UI=\"D006801\">Humans</DescriptorName>\n </MeshHeading>\n </MeshHeadingList>\n </MedlineCitation>\n <PubmedData>\n <History>\n <PubMedPubDate PubStatus=\"entrez\">\n <Year>2010</Year>\n <Month>8</Month>\n <Day>24</Day>\n <Hour>6</Hour>\n <Minute>0</Minute>\n </PubMedPubDate>\n <PubMedPubDate PubStatus=\"pubmed\">\n <Year>2010</Year>\n <Month>8</Month>\n <Day>24</Day>\n <Hour>6</Hour>\n <Minute>0</Minute>\n </PubMedPubDate>\n <PubMedPubDate PubStatus=\"medline\">\n <Year>2010</Year>\n <Month>12</Month>\n <Day>22</Day>\n <Hour>6</Hour>\n <Minute>0</Minute>\n </PubMedPubDate>\n </History>\n <PublicationStatus>ppublish</PublicationStatus>\n <ArticleIdList>\n <ArticleId IdType=\"doi\">10.1097/NNE.0b013e3181ed81e4</ArticleId>\n <ArticleId IdType=\"pii\">00006223-201009000-00011</ArticleId>\n <ArticleId IdType=\"pubmed\">20729678</ArticleId>\n </ArticleIdList>\n </PubmedData>\n</PubmedArticle>\n\n</PubmedArticleSet>\n",
"items": [
{
"itemType": "journalArticle",
"title": "Zotero: harnessing the power of a personal bibliographic manager",
"creators": [
{
"firstName": "Jaekea T.",
"lastName": "Coar",
"creatorType": "author"
},
{
"firstName": "Jeanne P.",
"lastName": "Sewell",
"creatorType": "author"
}
],
"date": "2010 Sep-Oct",
"DOI": "10.1097/NNE.0b013e3181ed81e4",
"ISSN": "1538-9855",
"abstractNote": "Zotero is a powerful free personal bibliographic manager (PBM) for writers. Use of a PBM allows the writer to focus on content, rather than the tedious details of formatting citations and references. Zotero 2.0 (http://www.zotero.org) has new features including the ability to synchronize citations with the off-site Zotero server and the ability to collaborate and share with others. An overview on how to use the software and discussion about the strengths and limitations are included.",
"extra": "PMID: 20729678",
"issue": "5",
"journalAbbreviation": "Nurse Educ",
"language": "eng",
"pages": "205-207",
"publicationTitle": "Nurse Educator",
"volume": "35",
"attachments": [
{
"title": "PubMed entry",
"mimeType": "text/html",
"snapshot": false
}
],
"tags": [
"Bibliography as Topic",
"Database Management Systems",
"Humans"
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "import",
"input": "<?xml version=\"1.0\"?>\n<!DOCTYPE PubmedArticleSet PUBLIC \"-//NLM//DTD PubMedArticle, 1st January 2015//EN\" \"http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_150101.dtd\">\n<PubmedArticleSet>\n<PubmedArticle>\n <MedlineCitation Owner=\"NLM\" Status=\"MEDLINE\">\n <PMID Version=\"1\">18157122</PMID>\n <DateCreated>\n <Year>2008</Year>\n <Month>01</Month>\n <Day>18</Day>\n </DateCreated>\n <DateCompleted>\n <Year>2008</Year>\n <Month>02</Month>\n <Day>08</Day>\n </DateCompleted>\n <DateRevised>\n <Year>2014</Year>\n <Month>07</Month>\n <Day>25</Day>\n </DateRevised>\n <Article PubModel=\"Print-Electronic\">\n <Journal>\n <ISSN IssnType=\"Electronic\">1552-4469</ISSN>\n <JournalIssue CitedMedium=\"Internet\">\n <Volume>4</Volume>\n <Issue>2</Issue>\n <PubDate>\n <Year>2008</Year>\n <Month>Feb</Month>\n </PubDate>\n </JournalIssue>\n <Title>Nature chemical biology</Title>\n <ISOAbbreviation>Nat. Chem. Biol.</ISOAbbreviation>\n </Journal>\n <ArticleTitle>High-content single-cell drug screening with phosphospecific flow cytometry.</ArticleTitle>\n <Pagination>\n <MedlinePgn>132-42</MedlinePgn>\n </Pagination>\n <Abstract>\n <AbstractText>Drug screening is often limited to cell-free assays involving purified enzymes, but it is arguably best applied against systems that represent disease states or complex physiological cellular networks. Here, we describe a high-content, cell-based drug discovery platform based on phosphospecific flow cytometry, or phosphoflow, that enabled screening for inhibitors against multiple endogenous kinase signaling pathways in heterogeneous primary cell populations at the single-cell level. From a library of small-molecule natural products, we identified pathway-selective inhibitors of Jak-Stat and MAP kinase signaling. Dose-response experiments in primary cells confirmed pathway selectivity, but importantly also revealed differential inhibition of cell types and new druggability trends across multiple compounds. Lead compound selectivity was confirmed in vivo in mice. Phosphoflow therefore provides a unique platform that can be applied throughout the drug discovery process, from early compound screening to in vivo testing and clinical monitoring of drug efficacy.</AbstractText>\n </Abstract>\n <AuthorList CompleteYN=\"Y\">\n <Author ValidYN=\"Y\">\n <LastName>Krutzik</LastName>\n <ForeName>Peter O</ForeName>\n <Initials>PO</Initials>\n <AffiliationInfo>\n <Affiliation>Department of Microbiology and Immunology, Baxter Laboratory in Genetic Pharmacology, Stanford University, 269 Campus Drive, Stanford, California 94305, USA.</Affiliation>\n </AffiliationInfo>\n </Author>\n <Author ValidYN=\"Y\">\n <LastName>Crane</LastName>\n <ForeName>Janelle M</ForeName>\n <Initials>JM</Initials>\n </Author>\n <Author ValidYN=\"Y\">\n <LastName>Clutter</LastName>\n <ForeName>Matthew R</ForeName>\n <Initials>MR</Initials>\n </Author>\n <Author ValidYN=\"Y\">\n <LastName>Nolan</LastName>\n <ForeName>Garry P</ForeName>\n <Initials>GP</Initials>\n </Author>\n 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