A Martel format to parse the NLM's XML format for Medline.
http://www.nlm.nih.gov/databases/dtd/nlmmedline_031101.dtd
http://www.nlm.nih.gov/databases/dtd/nlmmedlinecitation_031101.dtd
http://www.nlm.nih.gov/databases/dtd/nlmcommon_031101.dtd
Formats: citation_format Format for one MedlineCitation. format
Format for a whole file.
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OSpaces = Opt(Spaces())
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personal_name = LastName+ Opt(Alt(ForeName, FirstName+ Opt(Mid...
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author_name = Alt(personal_name, CollectiveName)
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imprint_type = Alt(Str("Current"), Str("Original"))
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indexing_status = Alt(Str("Ceased-publication"), Str("Continue...
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elements = [ ' Year ' , ' Month ' , ' Day ' , ' Season ' , ' MedlineDate ' , ' ...
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normal_date = Year+ Month+ Day+ Opt(Hour+ Opt(Minute+ Opt(Seco...
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pub_date = Alt((Year+ Opt(Alt((Month+ Opt(Day)), Season))), Me...
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Ref_template = RefSource+ Opt(Alt(PMID, MedlineID))+ Opt(Note)
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space = Any(" \t")
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DeleteCitation_start = Rep(space)+ Str("<DeleteCitation>")+ An...
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DeleteCitation_end = Rep(space)+ Str("</DeleteCitation>")+ Any...
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MedlineCitationSet_end = Str("</MedlineCitationSet>")+ Opt(Any...
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xml_version = Str('<?xml version="1.0"?>')+ AnyEol()
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doctype = Str('<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD ...
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pubmed_query_format = xml_version+ doctype+ PubmedArticleSet
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DOCTYPE = Str("<!DOCTYPE")+ Re(r"[^>]+")+ Str(">")+ AnyEol()
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citation_format = MedlineCitation
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header_format = Group("header", DOCTYPE+ MedlineCitationSet_st...
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footer_format = Opt(DeleteCitation)+ MedlineCitationSet_end
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format = HeaderFooter("MedlineFile", {}, header_format, Record...
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Abstract = <Martel.Expression.Group instance at 0x5962a28>
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AbstractText = <Martel.Expression.Seq instance at 0x59627e8>
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Abstract_end = <Martel.Expression.Seq instance at 0x59629e0>
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Abstract_start = <Martel.Expression.Seq instance at 0x5962908>
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AccessionNumber = <Martel.Expression.Seq instance at 0x596c758>
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AccessionNumberList = <Martel.Expression.Group instance at 0x5...
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AccessionNumberList_end = <Martel.Expression.Seq instance at 0...
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AccessionNumberList_start = <Martel.Expression.Seq instance at...
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Acronym = <Martel.Expression.Seq instance at 0x596a830>
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Affiliation = <Martel.Expression.Seq instance at 0x5965cf8>
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Agency = <Martel.Expression.Seq instance at 0x596aa70>
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Article = <Martel.Expression.Group instance at 0x596db00>
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ArticleId = <Martel.Expression.Seq instance at 0x597c128>
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ArticleIdList = <Martel.Expression.Group instance at 0x597c368>
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ArticleIdList_end = <Martel.Expression.Seq instance at 0x597c320>
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ArticleIdList_start = <Martel.Expression.Seq instance at 0x597...
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ArticleTitle = <Martel.Expression.Seq instance at 0x59679e0>
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Article_end = <Martel.Expression.Seq instance at 0x596dab8>
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Article_start = <Martel.Expression.Seq instance at 0x596d9e0>
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Author = <Martel.Expression.Group instance at 0x5965f38>
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AuthorList = <Martel.Expression.Group instance at 0x5966638>
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AuthorList_end = <Martel.Expression.Seq instance at 0x59665f0>
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AuthorList_start = <Martel.Expression.Seq instance at 0x5966560>
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Author_end = <Martel.Expression.Seq instance at 0x5965ef0>
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Author_start = <Martel.Expression.Seq instance at 0x5965e18>
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Book = <Martel.Expression.Group instance at 0x59681b8>
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Book_end = <Martel.Expression.Seq instance at 0x5968170>
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Book_start = <Martel.Expression.Seq instance at 0x5968098>
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Chemical = <Martel.Expression.Group instance at 0x5972f38>
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ChemicalList = <Martel.Expression.Group instance at 0x5974200>
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ChemicalList_end = <Martel.Expression.Seq instance at 0x59741b8>
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ChemicalList_start = <Martel.Expression.Seq instance at 0x5974...
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Chemical_end = <Martel.Expression.Seq instance at 0x5972ef0>
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Chemical_start = <Martel.Expression.Seq instance at 0x5972e18>
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CitationSubset = <Martel.Expression.Seq instance at 0x5974518>
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Coden = <Martel.Expression.Seq instance at 0x59693f8>
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CollectionTitle = <Martel.Expression.Seq instance at 0x59677a0>
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CollectiveName = <Martel.Expression.Seq instance at 0x595f878>
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CommentIn = <Martel.Expression.Group instance at 0x596efc8>
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CommentIn_end = <Martel.Expression.Seq instance at 0x596ef80>
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CommentIn_start = <Martel.Expression.Seq instance at 0x596eea8>
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CommentOn = <Martel.Expression.Group instance at 0x596ed40>
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CommentOn_end = <Martel.Expression.Seq instance at 0x596ecf8>
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CommentOn_start = <Martel.Expression.Seq instance at 0x596ec20>
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CommentsCorrections = <Martel.Expression.Group instance at 0x5...
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CommentsCorrections_end = <Martel.Expression.Seq instance at 0...
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CommentsCorrections_start = <Martel.Expression.Seq instance at...
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CopyrightInformation = <Martel.Expression.Seq instance at 0x59...
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Country = <Martel.Expression.Seq instance at 0x5968488>
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DataBank = <Martel.Expression.Group instance at 0x596cea8>
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DataBankList = <Martel.Expression.Group instance at 0x596d5a8>
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DataBankList_end = <Martel.Expression.Seq instance at 0x596d560>
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DataBankList_start = <Martel.Expression.Seq instance at 0x596d...
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DataBankName = <Martel.Expression.Seq instance at 0x596cc68>
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DataBank_end = <Martel.Expression.Seq instance at 0x596ce60>
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DataBank_start = <Martel.Expression.Seq instance at 0x596cd88>
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DateCompleted = <Martel.Expression.Group instance at 0x5979368>
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DateCompleted_end = <Martel.Expression.Seq instance at 0x5979320>
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DateCompleted_start = <Martel.Expression.Seq instance at 0x597...
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DateCreated = <Martel.Expression.Group instance at 0x59795f0>
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DateCreated_end = <Martel.Expression.Seq instance at 0x59795a8>
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DateCreated_start = <Martel.Expression.Seq instance at 0x59794d0>
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DateOfElectronicPublication = <Martel.Expression.Seq instance ...
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DateRevised = <Martel.Expression.Group instance at 0x59790e0>
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DateRevised_end = <Martel.Expression.Seq instance at 0x5979098>
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DateRevised_start = <Martel.Expression.Seq instance at 0x5976f80>
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Day = <Martel.Expression.Seq instance at 0x5961488>
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DeleteCitation = <Martel.Expression.Group instance at 0x5978998>
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Descriptor = <Martel.Expression.Seq instance at 0x5964368>
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DescriptorName = <Martel.Expression.Seq instance at 0x59649e0>
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EndPage = <Martel.Expression.Seq instance at 0x59654d0>
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ErratumFor = <Martel.Expression.Group instance at 0x5970518>
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ErratumFor_end = <Martel.Expression.Seq instance at 0x59704d0>
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ErratumFor_start = <Martel.Expression.Seq instance at 0x59703f8>
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ErratumIn = <Martel.Expression.Group instance at 0x5970290>
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ErratumIn_end = <Martel.Expression.Seq instance at 0x5970248>
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ErratumIn_start = <Martel.Expression.Seq instance at 0x5970170>
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FirstName = <Martel.Expression.Seq instance at 0x595eab8>
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ForeName = <Martel.Expression.Seq instance at 0x595ecf8>
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GeneSymbol = <Martel.Expression.Seq instance at 0x59725f0>
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GeneSymbolList = <Martel.Expression.Group instance at 0x59727e8>
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GeneSymbolList_end = <Martel.Expression.Seq instance at 0x5972...
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GeneSymbolList_start = <Martel.Expression.Seq instance at 0x59...
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GeneralNote = <Martel.Expression.Seq instance at 0x5974bd8>
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Grant = <Martel.Expression.Group instance at 0x596ad40>
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GrantID = <Martel.Expression.Seq instance at 0x596a5f0>
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GrantList = <Martel.Expression.Group instance at 0x596c440>
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GrantList_end = <Martel.Expression.Seq instance at 0x596c3f8>
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GrantList_start = <Martel.Expression.Seq instance at 0x596c368>
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Grant_end = <Martel.Expression.Seq instance at 0x596acf8>
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Grant_start = <Martel.Expression.Seq instance at 0x596ac20>
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History = <Martel.Expression.Group instance at 0x597a758>
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History_end = <Martel.Expression.Seq instance at 0x597a710>
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History_start = <Martel.Expression.Seq instance at 0x597a638>
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Hour = <Martel.Expression.Seq instance at 0x5961b48>
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ISOAbbreviation = <Martel.Expression.Seq instance at 0x59691b8>
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ISSN = <Martel.Expression.Seq instance at 0x5969fc8>
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Initials = <Martel.Expression.Seq instance at 0x595f3f8>
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Investigator = <Martel.Expression.Group instance at 0x5974dd0>
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InvestigatorList = <Martel.Expression.Group instance at 0x5975...
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InvestigatorList_end = <Martel.Expression.Seq instance at 0x59...
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InvestigatorList_start = <Martel.Expression.Seq instance at 0x...
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Investigator_end = <Martel.Expression.Seq instance at 0x5974d88>
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Investigator_start = <Martel.Expression.Seq instance at 0x5974...
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Issue = <Martel.Expression.Seq instance at 0x5969638>
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Journal = <Martel.Expression.Group instance at 0x596a320>
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JournalIssue = <Martel.Expression.Group instance at 0x5969cf8>
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JournalIssue_end = <Martel.Expression.Seq instance at 0x5969cb0>
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JournalIssue_start = <Martel.Expression.Seq instance at 0x5969...
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Journal_end = <Martel.Expression.Seq instance at 0x596a2d8>
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Journal_start = <Martel.Expression.Seq instance at 0x596a200>
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Keyword = <Martel.Expression.Seq instance at 0x5976128>
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KeywordList = <Martel.Expression.Group instance at 0x5976710>
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KeywordList_end = <Martel.Expression.Seq instance at 0x59766c8>
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KeywordList_start = <Martel.Expression.Seq instance at 0x5976638>
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Language = <Martel.Expression.Seq instance at 0x5966950>
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LastName = <Martel.Expression.Seq instance at 0x595f1b8>
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MedlineCitation = MedlineCitation
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MedlineCitationSet = <Martel.Expression.Group instance at 0x59...
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MedlineCitationSet_start = <Martel.Expression.Seq instance at ...
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MedlineCitation_end = <Martel.Expression.Seq instance at 0x597...
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MedlineCitation_start = <Martel.Expression.Seq instance at 0x5...
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MedlineCode = <Martel.Expression.Seq instance at 0x5968908>
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MedlineDate = <Martel.Expression.Seq instance at 0x5961908>
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MedlineID = <Martel.Expression.Seq instance at 0x596e0e0>
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MedlineJournalInfo = <Martel.Expression.Group instance at 0x59...
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MedlineJournalInfo_end = <Martel.Expression.Seq instance at 0x...
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MedlineJournalInfo_start = <Martel.Expression.Seq instance at ...
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MedlinePgn = <Martel.Expression.Seq instance at 0x5965290>
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MedlineTA = <Martel.Expression.Seq instance at 0x59686c8>
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MeshHeading = <Martel.Expression.Group instance at 0x5964cb0>
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MeshHeadingList = <Martel.Expression.Group instance at 0x5964f38>
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MeshHeadingList_end = <Martel.Expression.Seq instance at 0x596...
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MeshHeadingList_start = <Martel.Expression.Seq instance at 0x5...
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MeshHeading_end = <Martel.Expression.Seq instance at 0x5964c68>
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MeshHeading_start = <Martel.Expression.Seq instance at 0x5964b90>
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MiddleName = <Martel.Expression.Seq instance at 0x595ef38>
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Minute = <Martel.Expression.Seq instance at 0x5961d88>
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Month = <Martel.Expression.Seq instance at 0x5961248>
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NCBIArticle = <Martel.Expression.Group instance at 0x596ddd0>
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NCBIArticle_end = <Martel.Expression.Seq instance at 0x596dd88>
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NCBIArticle_start = <Martel.Expression.Seq instance at 0x596dcb0>
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NameOfSubstance = <Martel.Expression.Seq instance at 0x5972b00>
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NlmUniqueID = <Martel.Expression.Seq instance at 0x5962cf8>
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Note = <Martel.Expression.Seq instance at 0x596e320>
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NumberOfReferences = <Martel.Expression.Seq instance at 0x5971...
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OriginalReportIn = <Martel.Expression.Group instance at 0x596e...
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OriginalReportIn_end = <Martel.Expression.Seq instance at 0x59...
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OriginalReportIn_start = <Martel.Expression.Seq instance at 0x...
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OtherAbstract = <Martel.Expression.Group instance at 0x5976e60>
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OtherAbstract_end = <Martel.Expression.Seq instance at 0x5976e18>
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OtherAbstract_start = <Martel.Expression.Seq instance at 0x597...
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OtherID = <Martel.Expression.Seq instance at 0x5975830>
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PMID = <Martel.Expression.Seq instance at 0x5962f38>
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Pagination = <Martel.Expression.Group instance at 0x59659e0>
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Pagination_end = <Martel.Expression.Seq instance at 0x5965998>
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Pagination_start = <Martel.Expression.Seq instance at 0x59658c0>
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PersonalNameSubject = <Martel.Expression.Group instance at 0x5...
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PersonalNameSubjectList = <Martel.Expression.Group instance at...
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PersonalNameSubjectList_end = <Martel.Expression.Seq instance ...
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PersonalNameSubjectList_start = <Martel.Expression.Seq instanc...
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PersonalNameSubject_end = <Martel.Expression.Seq instance at 0...
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PersonalNameSubject_start = <Martel.Expression.Seq instance at...
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PubDate = <Martel.Expression.Group instance at 0x5967dd0>
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PubDate_end = <Martel.Expression.Seq instance at 0x5967d88>
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PubDate_start = <Martel.Expression.Seq instance at 0x5967cb0>
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PubMedPubDate = <Martel.Expression.Group instance at 0x597a440>
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PubMedPubDate_end = <Martel.Expression.Seq instance at 0x597a3f8>
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PubMedPubDate_start = <Martel.Expression.Seq instance at 0x597...
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PublicationStatus = <Martel.Expression.Seq instance at 0x597aa28>
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PublicationType = <Martel.Expression.Seq instance at 0x5966b90>
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PublicationTypeList = <Martel.Expression.Group instance at 0x5...
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PublicationTypeList_end = <Martel.Expression.Seq instance at 0...
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PublicationTypeList_start = <Martel.Expression.Seq instance at...
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Publisher = <Martel.Expression.Seq instance at 0x5967c20>
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PubmedArticle = <Martel.Expression.Group instance at 0x597c878>
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PubmedArticleSet = <Martel.Expression.Group instance at 0x597c...
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PubmedArticleSet_end = <Martel.Expression.Seq instance at 0x59...
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PubmedArticleSet_start = <Martel.Expression.Seq instance at 0x...
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PubmedArticle_end = <Martel.Expression.Seq instance at 0x597c830>
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PubmedArticle_start = <Martel.Expression.Seq instance at 0x597...
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PubmedData = <Martel.Expression.Group instance at 0x597c5f0>
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PubmedData_end = <Martel.Expression.Seq instance at 0x597c5a8>
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PubmedData_start = <Martel.Expression.Seq instance at 0x597c4d0>
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QualifierName = <Martel.Expression.Seq instance at 0x5963cb0>
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RefSource = <Martel.Expression.Seq instance at 0x596e560>
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RegistryNumber = <Martel.Expression.Seq instance at 0x5972d40>
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RepublishedFrom = <Martel.Expression.Group instance at 0x59707a0>
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RepublishedFrom_end = <Martel.Expression.Seq instance at 0x597...
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RepublishedFrom_start = <Martel.Expression.Seq instance at 0x5...
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RepublishedIn = <Martel.Expression.Group instance at 0x5970a28>
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RepublishedIn_end = <Martel.Expression.Seq instance at 0x59709e0>
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RepublishedIn_start = <Martel.Expression.Seq instance at 0x597...
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RetractionIn = <Martel.Expression.Group instance at 0x5970f38>
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RetractionIn_end = <Martel.Expression.Seq instance at 0x5970ef0>
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RetractionIn_start = <Martel.Expression.Seq instance at 0x5970...
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RetractionOf = <Martel.Expression.Group instance at 0x5970cb0>
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RetractionOf_end = <Martel.Expression.Seq instance at 0x5970c68>
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RetractionOf_start = <Martel.Expression.Seq instance at 0x5970...
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Season = <Martel.Expression.Seq instance at 0x59616c8>
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Second = <Martel.Expression.Seq instance at 0x5961fc8>
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SpaceFlightMission = <Martel.Expression.Seq instance at 0x5975...
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StartPage = <Martel.Expression.Seq instance at 0x5965710>
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SubHeading = <Martel.Expression.Seq instance at 0x5963638>
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Suffix = <Martel.Expression.Seq instance at 0x595f638>
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SummaryForPatientsIn = <Martel.Expression.Group instance at 0x...
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SummaryForPatientsIn_end = <Martel.Expression.Seq instance at ...
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SummaryForPatientsIn_start = <Martel.Expression.Seq instance a...
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Title = <Martel.Expression.Seq instance at 0x59670e0>
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UpdateIn = <Martel.Expression.Group instance at 0x5971200>
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UpdateIn_end = <Martel.Expression.Seq instance at 0x59711b8>
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UpdateIn_start = <Martel.Expression.Seq instance at 0x59710e0>
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UpdateOf = <Martel.Expression.Group instance at 0x5971488>
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UpdateOf_end = <Martel.Expression.Seq instance at 0x5971440>
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UpdateOf_start = <Martel.Expression.Seq instance at 0x5971368>
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VernacularTitle = <Martel.Expression.Seq instance at 0x5967560>
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Volume = <Martel.Expression.Seq instance at 0x5967320>
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Year = <Martel.Expression.Seq instance at 0x595ffc8>
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__warningregistry__ = { ( ' Bio.Medline.NLMMedlineXML was depreca ...
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e = ' Second '
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