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BibTeX Parser/Lexer: undesirable error for PubMedXML transformed data which contains email addresses #72

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GerHobbelt opened this issue Oct 1, 2019 · 0 comments
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GerHobbelt commented Oct 1, 2019

While the BibTeX documentation specifically states that % is not recognized as a comment character by BibTeX, it should be nice to have Qiqqa at least tolerate such input without b0rking as Qiqqa produces such non-compliant data itself when you grab a PubMedXML metadata XML record, which is then transformed into this BibTeX by Qiqqa itself:

(note the Parse Error mentioned at the bottom of this example)

@comment { BIBTEX_AUTO - GS }
@article{pmid:28129109,
  title={Motor-Coordinative and Cognitive Dysfunction Caused by Mutant TDP-43 Could Be Reversed by Inhibiting Its Mitochondrial Localization.},
  author={Wang, Wenzhang and Arakawa, Hiroyuki and Wang, Luwen and Okolo, Ogoegbunam and Siedlak, Sandra L and Jiang, Yinfei and Gao, Ju and Xie, Fei and Petersen, Robert B and Wang, Xinglong},
  journal={Molecular therapy : the journal of the American Society of Gene Therapy},
  journal-iso={Mol. Ther.},
  volume={25},
  number={1},
  year={2017},
  month={01},
  pages={127--139},
  doi={10.1016/j.ymthe.2016.10.013},
  pmid={28129109},
  abstract={Dominant missense mutations in TAR DNA-binding protein 43 (TDP-43) cause amyotrophic lateral sclerosis (ALS), and the cytoplasmic accumulation of TDP-43 represents a pathological hallmark in ALS and frontotemporal lobar degeneration (FTD). Behavioral investigation of the transgenic mouse model expressing the disease-causing human TDP-43 M337V mutant (TDP-43M337V mice) is encumbered by premature death in homozygous transgenic mice and a reported lack of phenotype assessed by tail elevation and footprint in hemizygous transgenic mice. Here, using a battery of motor-coordinative and cognitive tests, we report robust motor-coordinative and cognitive deficits in hemizygous TDP-43M337V mice by 8 months of age. After 12 months of age, cortical neurons are significantly affected by the mild expression of mutant TDP-43, characterized by cytoplasmic TDP-43 mislocalization, mitochondrial dysfunction, and neuronal loss. Compared with age-matched non-transgenic mice, TDP-43M337V mice demonstrate a similar expression of total TDP-43 but higher levels of TDP-43 in mitochondria. Interestingly, a TDP-43 mitochondrial localization inhibitory peptide abolishes cytoplasmic TDP-43 accumulation, restores mitochondrial function, prevents neuronal loss, and alleviates motor-coordinative and cognitive deficits in adult hemizygous TDP-43M337V mice. Thus, this study suggests hemizygous TDP-43M337V mice as a useful animal model to study TDP-43 toxicity and further consolidates mitochondrial TDP-43 as a novel therapeutic target for TDP-43-linked neurodegenerative diseases.Published by Elsevier Inc.}
}


% BEGIN:Original PubMed XML
%  <PubmedArticle>
%    <MedlineCitation Status="MEDLINE" Owner="NLM">
%      <PMID Version="1">28129109</PMID>
%      <DateCompleted>
%        <Year>2017</Year>
%        <Month>06</Month>
%        <Day>06</Day>
%      </DateCompleted>
%      <DateRevised>
%        <Year>2018</Year>
%        <Month>02</Month>
%        <Day>26</Day>
%      </DateRevised>
%      <Article PubModel="Print-Electronic">
%        <Journal>
%          <ISSN IssnType="Electronic">1525-0024</ISSN>
%          <JournalIssue CitedMedium="Internet">
%            <Volume>25</Volume>
%            <Issue>1</Issue>
%            <PubDate>
%              <Year>2017</Year>
%              <Month>01</Month>
%              <Day>04</Day>
%            </PubDate>
%          </JournalIssue>
%          <Title>Molecular therapy : the journal of the American Society of Gene Therapy</Title>
%          <ISOAbbreviation>Mol. Ther.</ISOAbbreviation>
%        </Journal>
%        <ArticleTitle>Motor-Coordinative and Cognitive Dysfunction Caused by Mutant TDP-43 Could Be Reversed by Inhibiting Its Mitochondrial Localization.</ArticleTitle>
%        <Pagination>
%          <MedlinePgn>127-139</MedlinePgn>
%        </Pagination>
%        <ELocationID EIdType="pii" ValidYN="Y">S1525-0016(16)45368-2</ELocationID>
%        <ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ymthe.2016.10.013</ELocationID>
%        <Abstract>
%          <AbstractText>Dominant missense mutations in TAR DNA-binding protein 43 (TDP-43) cause amyotrophic lateral sclerosis (ALS), and the cytoplasmic accumulation of TDP-43 represents a pathological hallmark in ALS and frontotemporal lobar degeneration (FTD). Behavioral investigation of the transgenic mouse model expressing the disease-causing human TDP-43 M337V mutant (TDP-43<sup>M337V</sup> mice) is encumbered by premature death in homozygous transgenic mice and a reported lack of phenotype assessed by tail elevation and footprint in hemizygous transgenic mice. Here, using a battery of motor-coordinative and cognitive tests, we report robust motor-coordinative and cognitive deficits in hemizygous TDP-43<sup>M337V</sup> mice by 8 months of age. After 12 months of age, cortical neurons are significantly affected by the mild expression of mutant TDP-43, characterized by cytoplasmic TDP-43 mislocalization, mitochondrial dysfunction, and neuronal loss. Compared with age-matched non-transgenic mice, TDP-43<sup>M337V</sup> mice demonstrate a similar expression of total TDP-43 but higher levels of TDP-43 in mitochondria. Interestingly, a TDP-43 mitochondrial localization inhibitory peptide abolishes cytoplasmic TDP-43 accumulation, restores mitochondrial function, prevents neuronal loss, and alleviates motor-coordinative and cognitive deficits in adult hemizygous TDP-43<sup>M337V</sup> mice. Thus, this study suggests hemizygous TDP-43<sup>M337V</sup> mice as a useful animal model to study TDP-43 toxicity and further consolidates mitochondrial TDP-43 as a novel therapeutic target for TDP-43-linked neurodegenerative diseases.</AbstractText>
%          <CopyrightInformation>Published by Elsevier Inc.</CopyrightInformation>
%        </Abstract>
%        <AuthorList CompleteYN="Y">
%          <Author ValidYN="Y">
%            <LastName>Wang</LastName>
%            <ForeName>Wenzhang</ForeName>
%            <Initials>W</Initials>
%            <AffiliationInfo>
%              <Affiliation>Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH 44106, USA.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%          <Author ValidYN="Y">
%            <LastName>Arakawa</LastName>
%            <ForeName>Hiroyuki</ForeName>
%            <Initials>H</Initials>
%            <AffiliationInfo>
%              <Affiliation>Rodent Behavioral Core, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%          <Author ValidYN="Y">
%            <LastName>Wang</LastName>
%            <ForeName>Luwen</ForeName>
%            <Initials>L</Initials>
%            <AffiliationInfo>
%              <Affiliation>Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH 44106, USA.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%          <Author ValidYN="Y">
%            <LastName>Okolo</LastName>
%            <ForeName>Ogoegbunam</ForeName>
%            <Initials>O</Initials>
%            <AffiliationInfo>
%              <Affiliation>Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH 44106, USA.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%          <Author ValidYN="Y">
%            <LastName>Siedlak</LastName>
%            <ForeName>Sandra L</ForeName>
%            <Initials>SL</Initials>
%            <AffiliationInfo>
%              <Affiliation>Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH 44106, USA.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%          <Author ValidYN="Y">
%            <LastName>Jiang</LastName>
%            <ForeName>Yinfei</ForeName>
%            <Initials>Y</Initials>
%            <AffiliationInfo>
%              <Affiliation>Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH 44106, USA.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%          <Author ValidYN="Y">
%            <LastName>Gao</LastName>
%            <ForeName>Ju</ForeName>
%            <Initials>J</Initials>
%            <AffiliationInfo>
%              <Affiliation>Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH 44106, USA.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%          <Author ValidYN="Y">
%            <LastName>Xie</LastName>
%            <ForeName>Fei</ForeName>
%            <Initials>F</Initials>
%            <AffiliationInfo>
%              <Affiliation>Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH 44106, USA.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%          <Author ValidYN="Y">
%            <LastName>Petersen</LastName>
%            <ForeName>Robert B</ForeName>
%            <Initials>RB</Initials>
%            <AffiliationInfo>
%              <Affiliation>Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH 44106, USA.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%          <Author ValidYN="Y">
%            <LastName>Wang</LastName>
%            <ForeName>Xinglong</ForeName>
%            <Initials>X</Initials>
%            <AffiliationInfo>
%              <Affiliation>Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH 44106, USA. Electronic address: xinglong.wang@case.edu.</Affiliation>
%            </AffiliationInfo>
%          </Author>
%        </AuthorList>
%        <Language>eng</Language>
%        <GrantList CompleteYN="Y">
%          <Grant>
%            <GrantID>R01 NS089604</GrantID>
%            <Acronym>NS</Acronym>
%            <Agency>NINDS NIH HHS</Agency>
%            <Country>United States</Country>
%          </Grant>
%        </GrantList>
%        <PublicationTypeList>
%          <PublicationType UI="D016428">Journal Article</PublicationType>
%          <PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType>
%        </PublicationTypeList>
%        <ArticleDate DateType="Electronic">
%          <Year>2017</Year>
%          <Month>01</Month>
%          <Day>04</Day>
%        </ArticleDate>
%      </Article>
%      <MedlineJournalInfo>
%        <Country>United States</Country>
%        <MedlineTA>Mol Ther</MedlineTA>
%        <NlmUniqueID>100890581</NlmUniqueID>
%        <ISSNLinking>1525-0016</ISSNLinking>
%      </MedlineJournalInfo>
%      <ChemicalList>
%        <Chemical>
%          <RegistryNumber>0</RegistryNumber>
%          <NameOfSubstance UI="D004268">DNA-Binding Proteins</NameOfSubstance>
%        </Chemical>
%        <Chemical>
%          <RegistryNumber>0</RegistryNumber>
%          <NameOfSubstance UI="D010446">Peptide Fragments</NameOfSubstance>
%        </Chemical>
%        <Chemical>
%          <RegistryNumber>0</RegistryNumber>
%          <NameOfSubstance UI="C578077">TDP-43 protein, mouse</NameOfSubstance>
%        </Chemical>
%      </ChemicalList>
%      <CitationSubset>IM</CitationSubset>
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%          <PMID Version="1">28129105</PMID>
%        </CommentsCorrections>
%      </CommentsCorrectionsList>
%      <MeshHeadingList>
%        <MeshHeading>
%          <DescriptorName UI="D000690" MajorTopicYN="N">Amyotrophic Lateral Sclerosis</DescriptorName>
%          <QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
%          <QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D001921" MajorTopicYN="N">Brain</DescriptorName>
%          <QualifierName UI="Q000166" MajorTopicYN="N">cytology</QualifierName>
%          <QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
%          <QualifierName UI="Q000473" MajorTopicYN="N">pathology</QualifierName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D060825" MajorTopicYN="N">Cognitive Dysfunction</DescriptorName>
%          <QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
%          <QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D004268" MajorTopicYN="N">DNA-Binding Proteins</DescriptorName>
%          <QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
%          <QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D008124" MajorTopicYN="N">Locomotion</DescriptorName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D051379" MajorTopicYN="N">Mice</DescriptorName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D008822" MajorTopicYN="N">Mice, Transgenic</DescriptorName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D008928" MajorTopicYN="N">Mitochondria</DescriptorName>
%          <QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
%          <QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D009043" MajorTopicYN="N">Motor Activity</DescriptorName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D053580" MajorTopicYN="N">Muscle Strength</DescriptorName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D009154" MajorTopicYN="Y">Mutation</DescriptorName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D009474" MajorTopicYN="N">Neurons</DescriptorName>
%          <QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D010446" MajorTopicYN="N">Peptide Fragments</DescriptorName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D021381" MajorTopicYN="N">Protein Transport</DescriptorName>
%        </MeshHeading>
%        <MeshHeading>
%          <DescriptorName UI="D011597" MajorTopicYN="Y">Psychomotor Performance</DescriptorName>
%        </MeshHeading>
%      </MeshHeadingList>
%      <KeywordList Owner="NOTNLM">
%        <Keyword MajorTopicYN="Y">ALS</Keyword>
%        <Keyword MajorTopicYN="Y">FTD</Keyword>
%        <Keyword MajorTopicYN="Y">TDP-43</Keyword>
%        <Keyword MajorTopicYN="Y">cognitive deficit</Keyword>
%        <Keyword MajorTopicYN="Y">mitochondrial dysfunction</Keyword>
%        <Keyword MajorTopicYN="Y">motor dysfunction</Keyword>
%        <Keyword MajorTopicYN="Y">neurodegeneration</Keyword>
%        <Keyword MajorTopicYN="Y">transgenic mice</Keyword>
%      </KeywordList>
%    </MedlineCitation>
%    <PubmedData>
%      <History>
%        <PubMedPubDate PubStatus="received">
%          <Year>2016</Year>
%          <Month>06</Month>
%          <Day>17</Day>
%        </PubMedPubDate>
%        <PubMedPubDate PubStatus="revised">
%          <Year>2016</Year>
%          <Month>10</Month>
%          <Day>10</Day>
%        </PubMedPubDate>
%        <PubMedPubDate PubStatus="accepted">
%          <Year>2016</Year>
%          <Month>10</Month>
%          <Day>21</Day>
%        </PubMedPubDate>
%        <PubMedPubDate PubStatus="entrez">
%          <Year>2017</Year>
%          <Month>1</Month>
%          <Day>28</Day>
%          <Hour>6</Hour>
%          <Minute>0</Minute>
%        </PubMedPubDate>
%        <PubMedPubDate PubStatus="pubmed">
%          <Year>2017</Year>
%          <Month>1</Month>
%          <Day>28</Day>
%          <Hour>6</Hour>
%          <Minute>0</Minute>
%        </PubMedPubDate>
%        <PubMedPubDate PubStatus="medline">
%          <Year>2017</Year>
%          <Month>6</Month>
%          <Day>7</Day>
%          <Hour>6</Hour>
%          <Minute>0</Minute>
%        </PubMedPubDate>
%      </History>
%      <PublicationStatus>ppublish</PublicationStatus>
%      <ArticleIdList>
%        <ArticleId IdType="pubmed">28129109</ArticleId>
%        <ArticleId IdType="pii">S1525-0016(16)45368-2</ArticleId>
%        <ArticleId IdType="doi">10.1016/j.ymthe.2016.10.013</ArticleId>
%        <ArticleId IdType="pmc">PMC5363201</ArticleId>
%      </ArticleIdList>
%    </PubmedData>
%  </PubmedArticle>
% END:Original PubMed XML

Parse Error:

Expecting a ( or {{ to start a BibTeX reference:

   . Electronic address: xinglong.wang@case.edu.</Affiliation>  %            </Affi
GerHobbelt added a commit to GerHobbelt/qiqqa-open-source that referenced this issue Oct 2, 2019
…tion macros in order to (somewhat) correctly parse google scholar patents records: fixes jimmejardine#22 and a bit of work towards jimmejardine#68
GerHobbelt added a commit to GerHobbelt/qiqqa-open-source that referenced this issue Oct 2, 2019
GerHobbelt added a commit to GerHobbelt/qiqqa-open-source that referenced this issue Oct 2, 2019
…tion macros in order to (somewhat) correctly parse google scholar patents records: fixes jimmejardine#22 and a bit of work towards jimmejardine#68

# Conflicts:
#	Utilities/BibTex/Parsing/BibTexLexer.cs
GerHobbelt added a commit to GerHobbelt/qiqqa-open-source that referenced this issue Oct 2, 2019
# Conflicts:
#	QiqqaSystemTester/data/fixtures/bibtex/b0rked-0008.bib
GerHobbelt added a commit to GerHobbelt/qiqqa-open-source that referenced this issue Oct 2, 2019
GerHobbelt added a commit to GerHobbelt/qiqqa-open-source that referenced this issue Oct 2, 2019
GerHobbelt added a commit to GerHobbelt/qiqqa-open-source that referenced this issue Oct 3, 2019
…tion macros in order to (somewhat) correctly parse google scholar patents records: fixes jimmejardine#22 and a bit of work towards jimmejardine#68

# Conflicts:
#	Utilities/BibTex/Parsing/BibTexLexer.cs
GerHobbelt added a commit to GerHobbelt/qiqqa-open-source that referenced this issue Oct 3, 2019
# Conflicts:
#	QiqqaSystemTester/data/fixtures/bibtex/b0rked-0008.bib
GerHobbelt added a commit to GerHobbelt/qiqqa-open-source that referenced this issue Oct 3, 2019
@GerHobbelt GerHobbelt added the 🐛bug Something isn't working label Oct 4, 2019
@GerHobbelt GerHobbelt added this to the v82 milestone Oct 9, 2019
@GerHobbelt GerHobbelt added this to To do in v82release Nov 3, 2019
GerHobbelt added a commit that referenced this issue Nov 5, 2019
GerHobbelt added a commit that referenced this issue Nov 5, 2019
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