Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations
Identifieur interne : 000400 ( Pmc/Curation ); précédent : 000399; suivant : 000401Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations
Auteurs : Steven Van Vooren [Belgique] ; Bernard Thienpont [Belgique] ; Björn Menten [Belgique] ; Frank Speleman [Belgique] ; Bart De Moor [Belgique] ; Joris Vermeesch [Belgique] ; Yves Moreau [Belgique]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2007.
Abstract
Biomedical literature provides a rich but unstructured source of associations between chromosomal regions and biomedical concepts. By mining MEDLINE abstracts, we annotate the human genome at the level of cytogenetic bands. Our method creates a set of chromosomal aberration maps that associate cytogenetic bands to biomedical concepts from a variety of controlled vocabularies, including disease, dysmorphology, anatomy, development and Gene Ontology branches. The association between a band (e.g. 4p16.3) and a concept (e.g. microcephaly) is assessed by the statistical overrepresentation of this concept in the abstracts relating to this band. Our method is validated using existing genome annotation resources and known chromosomal aberration maps and is further illustrated through a case study on heart disease. Our chromosomal aberration maps provide diagnostics support to clinical geneticists, aid cytogeneticists to interpret and report cytogenetic findings and support researchers interested in human gene function. The method is available as a web application, aBandApart, at
Url:
DOI: 10.1093/nar/gkm054
PubMed: 17403693
PubMed Central: 1885641
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Hospital, Herestraat 49, B-3000 Leuven, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Human Genetics, Leuven University Hospital, Herestraat 49, B-3000 Leuven</wicri:regionArea></affiliation></author><author><name sortKey="Moreau, Yves" sort="Moreau, Yves" uniqKey="Moreau Y" first="Yves" last="Moreau">Yves Moreau</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium,</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">17403693</idno><idno type="pmc">1885641</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885641</idno><idno type="RBID">PMC:1885641</idno><idno type="doi">10.1093/nar/gkm054</idno><date when="2007">2007</date><idno type="wicri:Area/Pmc/Corpus">000400</idno><idno type="wicri:Area/Pmc/Curation">000400</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations</title><author><name sortKey="Van Vooren, Steven" sort="Van Vooren, Steven" uniqKey="Van Vooren S" first="Steven" last="Van Vooren">Steven Van Vooren</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium,</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee</wicri:regionArea></affiliation></author><author><name sortKey="Thienpont, Bernard" sort="Thienpont, Bernard" uniqKey="Thienpont B" first="Bernard" last="Thienpont">Bernard Thienpont</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="AFF1">Center for Human Genetics, Leuven University Hospital, Herestraat 49, B-3000 Leuven, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Human Genetics, Leuven University Hospital, Herestraat 49, B-3000 Leuven</wicri:regionArea></affiliation></author><author><name sortKey="Menten, Bjorn" sort="Menten, Bjorn" uniqKey="Menten B" first="Björn" last="Menten">Björn Menten</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Center for Medical Genetics, Ghent University Hospital, MRB 2nd floor, De Pintelaan 185, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Medical Genetics, Ghent University Hospital, MRB 2nd floor, De Pintelaan 185, B-9000 Ghent</wicri:regionArea></affiliation></author><author><name sortKey="Speleman, Frank" sort="Speleman, Frank" uniqKey="Speleman F" first="Frank" last="Speleman">Frank Speleman</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Center for Medical Genetics, Ghent University Hospital, MRB 2nd floor, De Pintelaan 185, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Medical Genetics, Ghent University Hospital, MRB 2nd floor, De Pintelaan 185, B-9000 Ghent</wicri:regionArea></affiliation></author><author><name sortKey="Moor, Bart De" sort="Moor, Bart De" uniqKey="Moor B" first="Bart De" last="Moor">Bart De Moor</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium,</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee</wicri:regionArea></affiliation></author><author><name sortKey="Vermeesch, Joris" sort="Vermeesch, Joris" uniqKey="Vermeesch J" first="Joris" last="Vermeesch">Joris Vermeesch</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="AFF1">Center for Human Genetics, Leuven University Hospital, Herestraat 49, B-3000 Leuven, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Human Genetics, Leuven University Hospital, Herestraat 49, B-3000 Leuven</wicri:regionArea></affiliation></author><author><name sortKey="Moreau, Yves" sort="Moreau, Yves" uniqKey="Moreau Y" first="Yves" last="Moreau">Yves Moreau</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium,</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2007">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Biomedical literature provides a rich but unstructured source of associations between chromosomal regions and biomedical concepts. By mining MEDLINE abstracts, we annotate the human genome at the level of cytogenetic bands. Our method creates a set of chromosomal aberration maps that associate cytogenetic bands to biomedical concepts from a variety of controlled vocabularies, including disease, dysmorphology, anatomy, development and Gene Ontology branches. The association between a band (e.g. 4p16.3) and a concept (e.g. microcephaly) is assessed by the statistical overrepresentation of this concept in the abstracts relating to this band. Our method is validated using existing genome annotation resources and known chromosomal aberration maps and is further illustrated through a case study on heart disease. Our chromosomal aberration maps provide diagnostics support to clinical geneticists, aid cytogeneticists to interpret and report cytogenetic findings and support researchers interested in human gene function. The method is available as a web application, aBandApart, at <ext-link ext-link-type="uri" xlink:href="http://www.esat.kuleuven.be/abandapart/">http://www.esat.kuleuven.be/abandapart/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Brewer, C" uniqKey="Brewer C">C Brewer</name></author><author><name sortKey="Holloway, S" uniqKey="Holloway S">S Holloway</name></author><author><name sortKey="Zawalnyski, P" uniqKey="Zawalnyski P">P Zawalnyski</name></author><author><name sortKey="Schinzel, A" uniqKey="Schinzel A">A Schinzel</name></author><author><name sortKey="Fitzpatrick, D" uniqKey="Fitzpatrick D">D FitzPatrick</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brewer, C" uniqKey="Brewer C">C Brewer</name></author><author><name sortKey="Holloway, C" uniqKey="Holloway C">C Holloway</name></author><author><name sortKey="Zawalnyski, P" uniqKey="Zawalnyski P">P 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="pmc">nar</journal-id><journal-id journal-id-type="publisher-id">Nucleic Acids Research</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">17403693</article-id><article-id pub-id-type="pmc">1885641</article-id><article-id pub-id-type="doi">10.1093/nar/gkm054</article-id><article-categories><subj-group subj-group-type="heading"><subject>Computational Biology</subject></subj-group></article-categories><title-group><article-title>Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Van Vooren</surname><given-names>Steven</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Thienpont</surname><given-names>Bernard</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Menten</surname><given-names>Björn</given-names></name><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Speleman</surname><given-names>Frank</given-names></name><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Moor</surname><given-names>Bart De</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Vermeesch</surname><given-names>Joris</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Moreau</surname><given-names>Yves</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium,<sup>2</sup>Center for Human Genetics, Leuven University Hospital, Herestraat 49, B-3000 Leuven, Belgium and<sup>3</sup>Center for Medical Genetics, Ghent University Hospital, MRB 2nd floor, De Pintelaan 185, B-9000 Ghent, Belgium</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed <phone>+3216328654</phone><fax>+3216321970</fax><email>steven.vanvooren@esat.kuleuven.be</email></corresp></author-notes><pub-date pub-type="ppub"><month>4</month><year>2007</year></pub-date><pub-date pub-type="epub"><day>1</day><month>4</month><year>2007</year></pub-date><pub-date pub-type="pmc-release"><day>1</day><month>4</month><year>2007</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>35</volume><issue>8</issue><fpage>2533</fpage><lpage>2543</lpage><history><date date-type="received"><day>3</day><month>10</month><year>2006</year></date><date date-type="rev-recd"><day>27</day><month>10</month><year>2006</year></date><date date-type="accepted"><day>18</day><month>1</month><year>2007</year></date></history><permissions><copyright-statement>© 2007 The Author(s)</copyright-statement><copyright-year>2007</copyright-year><license license-type="open-access"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/">http://creativecommons.org/licenses/by-nc/2.0/uk/</ext-link>) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Biomedical literature provides a rich but unstructured source of associations between chromosomal regions and biomedical concepts. By mining MEDLINE abstracts, we annotate the human genome at the level of cytogenetic bands. Our method creates a set of chromosomal aberration maps that associate cytogenetic bands to biomedical concepts from a variety of controlled vocabularies, including disease, dysmorphology, anatomy, development and Gene Ontology branches. The association between a band (e.g. 4p16.3) and a concept (e.g. microcephaly) is assessed by the statistical overrepresentation of this concept in the abstracts relating to this band. Our method is validated using existing genome annotation resources and known chromosomal aberration maps and is further illustrated through a case study on heart disease. Our chromosomal aberration maps provide diagnostics support to clinical geneticists, aid cytogeneticists to interpret and report cytogenetic findings and support researchers interested in human gene function. The method is available as a web application, aBandApart, at <ext-link ext-link-type="uri" xlink:href="http://www.esat.kuleuven.be/abandapart/">http://www.esat.kuleuven.be/abandapart/</ext-link>.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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