Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations
Identifieur interne : 001432 ( Main/Exploration ); précédent : 001431; suivant : 001433Mapping 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
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000400
- to stream Pmc, to step Curation: 000400
- to stream Pmc, to step Checkpoint: 000431
- to stream Ncbi, to step Merge: 000021
- to stream Ncbi, to step Curation: 000021
- to stream Ncbi, to step Checkpoint: 000021
- to stream Main, to step Merge: 001437
- to stream Main, to step Curation: 001432
Le document en format XML
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Heverlee</wicri:noRegion></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><wicri:noRegion>B-3000 Leuven</wicri:noRegion></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, 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type="wicri:Area/Main/Exploration">001432</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><wicri:noRegion>B-3001 Heverlee</wicri:noRegion></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><wicri:noRegion>B-3000 Leuven</wicri:noRegion></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><wicri:noRegion>B-9000 Ghent</wicri:noRegion></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><wicri:noRegion>B-9000 Ghent</wicri:noRegion></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><wicri:noRegion>B-3001 Heverlee</wicri:noRegion></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><wicri:noRegion>B-3000 Leuven</wicri:noRegion></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><wicri:noRegion>B-3001 Heverlee</wicri:noRegion></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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Cil</name></author><author><name sortKey="Yapici, E" uniqKey="Yapici E">E Yapici</name></author><author><name sortKey="Egeli, U" uniqKey="Egeli U">U Egeli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krantz, Id" uniqKey="Krantz I">ID Krantz</name></author><author><name sortKey="Smith, R" uniqKey="Smith R">R Smith</name></author><author><name sortKey="Colliton, Rp" uniqKey="Colliton R">RP Colliton</name></author><author><name sortKey="Tinkel, H" uniqKey="Tinkel H">H Tinkel</name></author><author><name sortKey="Zackai, Eh" uniqKey="Zackai E">EH Zackai</name></author><author><name sortKey="Piccoli, Da" uniqKey="Piccoli D">DA Piccoli</name></author><author><name sortKey="Goldmuntz, E" uniqKey="Goldmuntz E">E Goldmuntz</name></author><author><name sortKey="Spinner, Nb" uniqKey="Spinner N">NB Spinner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kosaki, R" uniqKey="Kosaki R">R Kosaki</name></author><author><name sortKey="Kosaki, K" uniqKey="Kosaki K">K Kosaki</name></author><author><name sortKey="Matsushima, K" uniqKey="Matsushima K">K Matsushima</name></author><author><name sortKey="Mitsui, N" uniqKey="Mitsui N">N Mitsui</name></author><author><name sortKey="Matsumoto, N" uniqKey="Matsumoto N">N Matsumoto</name></author><author><name sortKey="Ohashi, H" uniqKey="Ohashi H">H Ohashi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Robinson, Wp" uniqKey="Robinson W">WP Robinson</name></author><author><name sortKey="Waslynka, J" uniqKey="Waslynka J">J Waslynka</name></author><author><name sortKey="Bernasconi, F" uniqKey="Bernasconi F">F Bernasconi</name></author><author><name sortKey="Wang, M" uniqKey="Wang M">M Wang</name></author><author><name sortKey="Clark, S" uniqKey="Clark S">S Clark</name></author><author><name sortKey="Kotzot, D" uniqKey="Kotzot D">D Kotzot</name></author><author><name sortKey="Schinzel, A" uniqKey="Schinzel A">A Schinzel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wren, Jd" uniqKey="Wren J">JD Wren</name></author><author><name sortKey="Hildebrand, Wh" uniqKey="Hildebrand W">WH Hildebrand</name></author><author><name sortKey="Chandrasekaran, S" uniqKey="Chandrasekaran S">S Chandrasekaran</name></author><author><name sortKey="Ulrich Melcher, U" uniqKey="Ulrich Melcher U">U Ulrich Melcher</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shah, Pk" uniqKey="Shah P">PK Shah</name></author><author><name sortKey="Perez Iratxeta, C" uniqKey="Perez Iratxeta C">C Perez-Iratxeta</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P Bork</name></author><author><name sortKey="Andrade, Ma" uniqKey="Andrade M">MA Andrade</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Belgique</li></country></list><tree><country name="Belgique"><noRegion><name sortKey="Van Vooren, Steven" sort="Van Vooren, Steven" uniqKey="Van Vooren S" first="Steven" last="Van Vooren">Steven Van Vooren</name></noRegion><name sortKey="Menten, Bjorn" sort="Menten, Bjorn" uniqKey="Menten B" first="Björn" last="Menten">Björn Menten</name><name sortKey="Moor, Bart De" sort="Moor, Bart De" uniqKey="Moor B" first="Bart De" last="Moor">Bart De Moor</name><name sortKey="Moreau, Yves" sort="Moreau, Yves" uniqKey="Moreau Y" first="Yves" last="Moreau">Yves Moreau</name><name sortKey="Speleman, Frank" sort="Speleman, Frank" uniqKey="Speleman F" first="Frank" last="Speleman">Frank Speleman</name><name sortKey="Thienpont, Bernard" sort="Thienpont, Bernard" uniqKey="Thienpont B" first="Bernard" last="Thienpont">Bernard Thienpont</name><name sortKey="Vermeesch, Joris" sort="Vermeesch, Joris" uniqKey="Vermeesch J" first="Joris" last="Vermeesch">Joris Vermeesch</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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