Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations
Identifieur interne : 000321 ( Pmc/Checkpoint ); précédent : 000320; suivant : 000322Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations
Auteurs : Sofie Van Landeghem [Belgique] ; Kai Hakala [Finlande] ; Samuel Rönnqvist [Finlande] ; Tapio Salakoski [Finlande] ; Yves Van De Peer [Belgique] ; Filip Ginter [Finlande]Source :
- Advances in Bioinformatics [ 1687-8027 ] ; 2012.
Abstract
Technological advancements in the field of genetics have led not only to an abundance of experimental data, but also caused an exponential increase of the number of published biomolecular studies. Text mining is widely accepted as a promising technique to help researchers in the life sciences deal with the amount of available literature. This paper presents a freely available web application built on top of 21.3 million detailed biomolecular events extracted from all PubMed abstracts. These text mining results were generated by a state-of-the-art event extraction system and enriched with gene family associations and abstract generalizations, accounting for lexical variants and synonymy. The EVEX resource locates relevant literature on phosphorylation, regulation targets, binding partners, and several other biomolecular events and assigns confidence values to these events. The search function accepts official gene/protein symbols as well as common names from all species. Finally, the web application is a powerful tool for generating homology-based hypotheses as well as novel, indirect associations between genes and proteins such as coregulators.
Url:
DOI: 10.1155/2012/582765
PubMed: 22719757
PubMed Central: 3375141
Affiliations:
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927, 9052 Gent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent</wicri:regionArea><wicri:noRegion>9052 Gent</wicri:noRegion></affiliation></author><author><name sortKey="Hakala, Kai" sort="Hakala, Kai" uniqKey="Hakala K" first="Kai" last="Hakala">Kai Hakala</name><affiliation wicri:level="4"><nlm:aff id="I3">Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation></author><author><name sortKey="Ronnqvist, Samuel" sort="Ronnqvist, Samuel" uniqKey="Ronnqvist S" first="Samuel" last="Rönnqvist">Samuel Rönnqvist</name><affiliation wicri:level="4"><nlm:aff id="I3">Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation></author><author><name sortKey="Salakoski, Tapio" sort="Salakoski, Tapio" uniqKey="Salakoski T" first="Tapio" last="Salakoski">Tapio Salakoski</name><affiliation wicri:level="4"><nlm:aff id="I3">Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I4">Turku BioNLP Group, Turku Centre for Computer Science (TUCS), Joukahaisenkatu 3-5, 20520 Turku, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Turku BioNLP Group, Turku Centre for Computer Science (TUCS), Joukahaisenkatu 3-5, 20520 Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation></author><author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent</wicri:regionArea><wicri:noRegion>9052 Gent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent</wicri:regionArea><wicri:noRegion>9052 Gent</wicri:noRegion></affiliation></author><author><name sortKey="Ginter, Filip" sort="Ginter, Filip" uniqKey="Ginter F" first="Filip" last="Ginter">Filip Ginter</name><affiliation wicri:level="4"><nlm:aff id="I3">Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation></author></analytic><series><title level="j">Advances in Bioinformatics</title><idno type="ISSN">1687-8027</idno><idno type="eISSN">1687-8035</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Technological advancements in the field of genetics have led not only to an abundance of experimental data, but also caused an exponential increase of the number of published biomolecular studies. Text mining is widely accepted as a promising technique to help researchers in the life sciences deal with the amount of available literature. This paper presents a freely available web application built on top of 21.3 million detailed biomolecular events extracted from all PubMed abstracts. These text mining results were generated by a state-of-the-art event extraction system and enriched with gene family associations and abstract generalizations, accounting for lexical variants and synonymy. The EVEX resource locates relevant literature on phosphorylation, regulation targets, binding partners, and several other biomolecular events and assigns confidence values to these events. The search function accepts official gene/protein symbols as well as common names from all species. Finally, the web application is a powerful tool for generating homology-based hypotheses as well as novel, indirect associations between genes and proteins such as coregulators.
</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kim, J D" uniqKey="Kim J">J-D Kim</name></author><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Kano, Y" uniqKey="Kano Y">Y Kano</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, J D" uniqKey="Kim J">J-D Kim</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Bossy N Nguyen, R" uniqKey="Bossy N Nguyen R">R Bossy, N. Nguyen</name></author><author><name sortKey="Nguyen, N" uniqKey="Nguyen N">N Nguyen</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Homann, R" uniqKey="Homann R">R Homann</name></author><author><name sortKey="Valencia, A" uniqKey="Valencia A">A Valencia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Miyao, Y" uniqKey="Miyao Y">Y Miyao</name></author><author><name sortKey="Ninomiya, T" uniqKey="Ninomiya T">T Ninomiya</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rebholz Schuhmann, D" uniqKey="Rebholz Schuhmann D">D Rebholz-Schuhmann</name></author><author><name sortKey="Kirsch, H" uniqKey="Kirsch H">H Kirsch</name></author><author><name sortKey="Arregui, M" uniqKey="Arregui M">M Arregui</name></author><author><name sortKey="Gaudan, S" uniqKey="Gaudan S">S Gaudan</name></author><author><name sortKey="Riethoven, M" uniqKey="Riethoven M">M Riethoven</name></author><author><name sortKey="Stoehr, P" uniqKey="Stoehr P">P Stoehr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hearst, Ma" uniqKey="Hearst M">MA Hearst</name></author><author><name sortKey="Divoli, A" uniqKey="Divoli A">A Divoli</name></author><author><name sortKey="Guturu, Hh" uniqKey="Guturu H">HH Guturu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, S" uniqKey="Xu S">S Xu</name></author><author><name sortKey="Mccusker, J" uniqKey="Mccusker J">J McCusker</name></author><author><name sortKey="Krauthammer, M" uniqKey="Krauthammer M">M Krauthammer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Agarwal, S" uniqKey="Agarwal S">S Agarwal</name></author><author><name sortKey="Yu, H" uniqKey="Yu H">H Yu</name></author><author><name sortKey="Kohane, I" uniqKey="Kohane I">I Kohane</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bjorne, J" uniqKey="Bjorne J">J Björne</name></author><author><name sortKey="Ginter, F" uniqKey="Ginter F">F Ginter</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author><author><name sortKey="Salakoski, T" uniqKey="Salakoski T">T Salakoski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Landeghem, S" uniqKey="Van Landeghem S">S Van Landeghem</name></author><author><name sortKey="Ginter, F" uniqKey="Ginter F">F Ginter</name></author><author><name sortKey="Van De Peer, Y" uniqKey="Van De Peer Y">Y Van de Peer</name></author><author><name sortKey="Salakoski, T" uniqKey="Salakoski T">T Salakoski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leaman, R" uniqKey="Leaman R">R Leaman</name></author><author><name sortKey="Gonzalez, G" uniqKey="Gonzalez G">G Gonzalez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bjorne, J" uniqKey="Bjorne J">J Björne</name></author><author><name sortKey="Ginter, F" uniqKey="Ginter F">F Ginter</name></author><author><name sortKey="Salakoski, T" uniqKey="Salakoski T">T Salakoski</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Sayers, Ew" uniqKey="Sayers E">EW Sayers</name></author><author><name sortKey="Barrett, T" uniqKey="Barrett T">T Barrett</name></author><author><name sortKey="Benson, Da" uniqKey="Benson D">DA Benson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Flicek, P" uniqKey="Flicek P">P Flicek</name></author><author><name sortKey="Amode, Mr" uniqKey="Amode M">MR Amode</name></author><author><name sortKey="Barrell, D" uniqKey="Barrell D">D Barrell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kersey, Pj" uniqKey="Kersey P">PJ Kersey</name></author><author><name sortKey="Lawson, D" uniqKey="Lawson D">D Lawson</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Crammer, K" uniqKey="Crammer K">K Crammer</name></author><author><name sortKey="Singer, Y" uniqKey="Singer Y">Y Singer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Segal, E" uniqKey="Segal E">E Segal</name></author><author><name sortKey="Shapira, M" uniqKey="Shapira M">M Shapira</name></author><author><name sortKey="Regev, A" uniqKey="Regev A">A Regev</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bjorne, J" uniqKey="Bjorne J">J Björne</name></author><author><name sortKey="Ginter, F" uniqKey="Ginter F">F Ginter</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author><author><name sortKey="Salakoski, T" uniqKey="Salakoski T">T Salakoski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kaewphan, S" uniqKey="Kaewphan S">S Kaewphan</name></author><author><name sortKey="Kreula, S" uniqKey="Kreula S">S Kreula</name></author><author><name sortKey="Van Landeghem, S" uniqKey="Van Landeghem S">S Van Landeghem</name></author><author><name sortKey="Van De Peer, Y" uniqKey="Van De Peer Y">Y Van de Peer</name></author><author><name sortKey="Jones, P" uniqKey="Jones P">P Jones</name></author><author><name sortKey="Ginter, F" uniqKey="Ginter F">F Ginter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carballo, Ja" uniqKey="Carballo J">JA Carballo</name></author><author><name sortKey="Cha, Rs" uniqKey="Cha R">RS Cha</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Loewenstein, Y" uniqKey="Loewenstein Y">Y Loewenstein</name></author><author><name sortKey="Raimondo, D" uniqKey="Raimondo D">D Raimondo</name></author><author><name sortKey="Redfern, Oc" uniqKey="Redfern O">OC Redfern</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Proost, S" uniqKey="Proost S">S Proost</name></author><author><name sortKey="Van Bel, M" uniqKey="Van Bel M">M Van Bel</name></author><author><name sortKey="Sterck, L" uniqKey="Sterck L">L Sterck</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kato, R" uniqKey="Kato R">R Kato</name></author><author><name sortKey="Ogawa, H" uniqKey="Ogawa H">H Ogawa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stenetorp, P" uniqKey="Stenetorp P">P Stenetorp</name></author><author><name sortKey="Topi, G" uniqKey="Topi G">G Topić</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Kim, J D" uniqKey="Kim J">J-D Kim</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bjorne, J" uniqKey="Bjorne J">J Björne</name></author><author><name sortKey="Salakoski, T" uniqKey="Salakoski T">T Salakoski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Landeghem, S" uniqKey="Van Landeghem S">S Van Landeghem</name></author><author><name sortKey="Bjorne, J" uniqKey="Bjorne J">J Björne</name></author><author><name sortKey="Abeel, T" uniqKey="Abeel T">T Abeel</name></author><author><name sortKey="De Baets, B" uniqKey="De Baets B">B De Baets</name></author><author><name sortKey="Salakoski, T" uniqKey="Salakoski T">T Salakoski</name></author><author><name sortKey="Van De Peer, Y" uniqKey="Van De Peer Y">Y Van de Peer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lu, Z" uniqKey="Lu Z">Z Lu</name></author><author><name sortKey="Kao, Hy" uniqKey="Kao H">HY Kao</name></author><author><name sortKey="Wei, Ch" uniqKey="Wei C">CH Wei</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Adv Bioinformatics</journal-id><journal-id journal-id-type="iso-abbrev">Adv Bioinformatics</journal-id><journal-id journal-id-type="publisher-id">ABI</journal-id><journal-title-group><journal-title>Advances in Bioinformatics</journal-title></journal-title-group><issn pub-type="ppub">1687-8027</issn><issn pub-type="epub">1687-8035</issn><publisher><publisher-name>Hindawi Publishing Corporation</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22719757</article-id><article-id pub-id-type="pmc">3375141</article-id><article-id pub-id-type="doi">10.1155/2012/582765</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Van Landeghem</surname><given-names>Sofie</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hakala</surname><given-names>Kai</given-names></name><xref ref-type="aff" rid="I3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rönnqvist</surname><given-names>Samuel</given-names></name><xref ref-type="aff" rid="I3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Salakoski</surname><given-names>Tapio</given-names></name><xref ref-type="aff" rid="I3"><sup>3</sup></xref><xref ref-type="aff" rid="I4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Van de Peer</surname><given-names>Yves</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ginter</surname><given-names>Filip</given-names></name><xref ref-type="aff" rid="I3"><sup>3</sup></xref><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff id="I1"><sup>1</sup>Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium</aff><aff id="I2"><sup>2</sup>Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium</aff><aff id="I3"><sup>3</sup>Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku, Finland</aff><aff id="I4"><sup>4</sup>Turku BioNLP Group, Turku Centre for Computer Science (TUCS), Joukahaisenkatu 3-5, 20520 Turku, Finland</aff><author-notes><corresp id="cor1">*Filip Ginter: <email>ginter@cs.utu.fi</email></corresp><fn fn-type="other"><p>Academic Editor: Jin-Dong Kim</p></fn></author-notes><pub-date pub-type="ppub"><year>2012</year></pub-date><pub-date pub-type="epub"><day>6</day><month>6</month><year>2012</year></pub-date><volume>2012</volume><elocation-id>582765</elocation-id><history><date date-type="received"><day>22</day><month>11</month><year>2011</year></date><date date-type="rev-recd"><day>16</day><month>3</month><year>2012</year></date><date date-type="accepted"><day>28</day><month>3</month><year>2012</year></date></history><permissions><copyright-statement>Copyright © 2012 Sofie Van Landeghem et al.</copyright-statement><copyright-year>2012</copyright-year><license license-type="open-access"><license-p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Technological advancements in the field of genetics have led not only to an abundance of experimental data, but also caused an exponential increase of the number of published biomolecular studies. Text mining is widely accepted as a promising technique to help researchers in the life sciences deal with the amount of available literature. This paper presents a freely available web application built on top of 21.3 million detailed biomolecular events extracted from all PubMed abstracts. These text mining results were generated by a state-of-the-art event extraction system and enriched with gene family associations and abstract generalizations, accounting for lexical variants and synonymy. The EVEX resource locates relevant literature on phosphorylation, regulation targets, binding partners, and several other biomolecular events and assigns confidence values to these events. The search function accepts official gene/protein symbols as well as common names from all species. Finally, the web application is a powerful tool for generating homology-based hypotheses as well as novel, indirect associations between genes and proteins such as coregulators.
</p></abstract></article-meta></front><floats-group><fig id="fig1" position="float"><label>Figure 1</label><caption><p>Event representation of the statement <italic>IL-2 acts by enhancing binding activity of NF-κB to p55</italic>, illustrating recursive nesting of events where the (T)heme of the <italic>positive regulation</italic> event is the <italic>binding</italic> event. The (C)ause argument is the gene symbol <italic>IL-2</italic> (figure adapted from [<xref ref-type="bibr" rid="B28">10</xref>]).</p></caption><graphic xlink:href="ABI2012-582765.001"></graphic></fig><fig id="fig2" position="float"><label>Figure 2</label><caption><p>Evaluation of predicted binding events, measured against the gold-standard data of the ST'09 development set. By sorting the events according to their confidence values, a tradeoff between precision and recall is obtained.</p></caption><graphic xlink:href="ABI2012-582765.002"></graphic></fig><fig id="fig3" position="float"><label>Figure 3</label><caption><p>Search results for <italic>Mec1</italic> on the canonical generalization. An overview of directly associated genes is presented, grouped by event type. In the screenshot, only the box with regulation targets is shown, but the other event types may also be expanded. At the bottom, relevant links to additional sentences and articles are provided.</p></caption><graphic xlink:href="ABI2012-582765.003"></graphic></fig><fig id="fig4" position="float"><label>Figure 4</label><caption><p>Detailed representation of all evidence supporting the regulation of RAD9 by Mec1. Regulatory mechanisms can have a certain polarity (positive/negative) and may involve physical events such as phosphorylation or protein-DNA binding.</p></caption><graphic xlink:href="ABI2012-582765.004"></graphic></fig><fig id="fig5" position="float"><label>Figure 5</label><caption><p>All events linking <italic>Mec1</italic> and <italic>RAD9</italic> through either direct or indirect associations. In the screenshot, only the regulation boxes are shown in detail, but the other event types may also be expanded. This page enables a quick overview of the mechanisms through which two genes interact, while at the same time highlighting false positive text mining results which can be identified by comparing confidence values and the evidence found in the sentences.</p></caption><graphic xlink:href="ABI2012-582765.005"></graphic></fig><fig id="fig6" position="float"><label>Figure 6</label><caption><p>Visualization of a specific event occurrence by the stav text annotation visualiser. Genes and gene products (“GGPs”) are marked, as well as the trigger words that refer to specific event types. Finally, arrows denote the roles of each argument in the event (e.g. Theme or Cause). This visualization corresponds to the formal bracketed format of the event: <italic>Positive-regulation(C: Mec1, T:Phosphorylation(T:RAD9))</italic>.</p></caption><graphic xlink:href="ABI2012-582765.006"></graphic></fig><table-wrap id="tab1" position="float"><label>Table 1</label><caption><p>Listing of the refinement rules, involving any nested combination of the three types of regulation: positive regulation (Pos), negative regulation (Neg) and unspecified regulation (Reg). Each parent event has a regulatory (T)heme argument and an optional (C)ause. The nested regulations are all regulations without a Cause and their detailed structure is omitted for brevity. In full, the first structure would read <italic>Pos(C:geneA, T:Pos(T:geneB))</italic> which is rewritten to <italic>Pos(C:geneA, T:geneB)</italic> with <italic>geneA</italic> and <italic>geneB</italic> being any two genes. </p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1"> Original</th><th align="center" rowspan="1" colspan="1"> Result</th><th align="center" rowspan="1" colspan="1"> Example</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><italic>Pos(C, T:Pos)</italic></td><td align="center" rowspan="1" colspan="1"><italic>Pos(C, T)</italic></td><td align="center" rowspan="1" colspan="1"> BRs induce accumulation of BZR1 protein</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Pos(C, T:Reg)</italic></td><td align="center" rowspan="1" colspan="1"><italic>Pos(C, T)</italic></td><td align="center" rowspan="1" colspan="1"> PKS5 mediates PM H +- ATPase regulation</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Reg(C, T:Pos)</italic></td><td align="center" rowspan="1" colspan="1"><italic>Pos(C, T)</italic></td><td align="center" rowspan="1" colspan="1"> CaM regulates activation of HSFs</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Neg(C, T:Neg)</italic></td><td align="center" rowspan="1" colspan="1"><italic>Pos(C, T)</italic></td><td align="center" rowspan="1" colspan="1"> E2 prevented downregulation of p21 </td></tr><tr><td align="left" colspan="3" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Reg(C, T:Reg)</italic></td><td align="center" rowspan="1" colspan="1"><italic>Reg(C, T)</italic></td><td align="center" rowspan="1" colspan="1"> PDK1 is involved in the regulation of S6K </td></tr><tr><td align="left" colspan="3" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Neg(C, T:Reg)</italic></td><td align="center" rowspan="1" colspan="1"><italic>Neg(C, T)</italic></td><td align="center" rowspan="1" colspan="1"> GW5074 prevents this effect on ENT1 mRNA</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Neg(C, T:Pos)</italic></td><td align="center" rowspan="1" colspan="1"><italic>Neg(C, T)</italic></td><td align="center" rowspan="1" colspan="1"> BIN2 negatively regulates BZR1 accumulation</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Reg(C, T:Neg)</italic></td><td align="center" rowspan="1" colspan="1"><italic>Neg(C, T)</italic></td><td align="center" rowspan="1" colspan="1"> The effect of hCG in downregulating ER beta</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Pos(C, T:Neg)</italic></td><td align="center" rowspan="1" colspan="1"><italic>Neg(C, T)</italic></td><td align="center" rowspan="1" colspan="1"> DtRE is required for repression of CAB2</td></tr></tbody></table></table-wrap><table-wrap id="tab2" position="float"><label>Table 2</label><caption><p>The most prevalent (refined) event patterns in the EVEX data, considering only events with more than one gene or protein symbol, and their recursively nested events. These aggregated patterns refer to any type of regulation (<italic>*Reg</italic>), to binding events between two genes (<italic>Bind</italic>), and to any physical event (<italic>Phy</italic>) concerning a single gene such as protein-DNA binding, protein catabolism, transcription, localization, phosphorylation, and gene expression. The first two columns refer to the percentage of event occurrences covered by the given pattern and the cumulative percentage of event occurrences up to and including the pattern. The right-most column depicts the extracted gene pair and a coarse classification of its association type. <italic>A</italic> and <italic>B</italic> refer to gene symbols, and bindings are represented with ×. Further, <italic>A</italic> > <italic>B</italic> means <italic>A regulates B,</italic> while <italic>A</italic> ≫ <italic>B</italic> expresses an indirect regulation. </p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1"> Occ. [%]</th><th align="center" rowspan="1" colspan="1"> Cum. occ. [%]</th><th align="center" rowspan="1" colspan="1"> Event pattern</th><th align="center" rowspan="1" colspan="1"> Gene pair</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"> 58.6</td><td align="center" rowspan="1" colspan="1"> 58.6</td><td align="center" rowspan="1" colspan="1"><italic>Phy(T:A)</italic></td><td align="center" rowspan="1" colspan="1"> —</td></tr><tr><td align="left" rowspan="1" colspan="1">15.0</td><td align="center" rowspan="1" colspan="1"> 73.6</td><td align="center" rowspan="1" colspan="1"><italic>*Reg(T:A)</italic></td><td align="center" rowspan="1" colspan="1"> —</td></tr><tr><td align="left" rowspan="1" colspan="1"> 8.4</td><td align="center" rowspan="1" colspan="1"> 82.0</td><td align="center" rowspan="1" colspan="1"><italic>*Reg(T:Phy(T:A))</italic></td><td align="center" rowspan="1" colspan="1">—</td></tr><tr><td align="left" rowspan="1" colspan="1"> 8.0</td><td align="center" rowspan="1" colspan="1"> 90.0</td><td align="center" rowspan="1" colspan="1"><italic>Bind(T:A, T:B)</italic></td><td align="center" rowspan="1" colspan="1"><italic>A</italic> × <italic>B</italic></td></tr><tr><td align="left" rowspan="1" colspan="1"> 4.7</td><td align="center" rowspan="1" colspan="1"> 94.7</td><td align="center" rowspan="1" colspan="1"><italic>*Reg(C:A, T:B)</italic></td><td align="center" rowspan="1" colspan="1"><italic>A</italic> > <italic>B</italic></td></tr><tr><td align="left" rowspan="1" colspan="1"> 3.8</td><td align="center" rowspan="1" colspan="1"> 98.5</td><td align="center" rowspan="1" colspan="1"><italic>*Reg(C:A, T:Phy(T:B))</italic></td><td align="center" rowspan="1" colspan="1"><italic>A</italic> > <italic>B</italic></td></tr><tr><td align="left" rowspan="1" colspan="1"> 0.2</td><td align="center" rowspan="1" colspan="1"> 98.7</td><td align="center" rowspan="1" colspan="1"><italic>*Reg(C:*Reg(T:Phy(T:A)), T:Phy(T:B))</italic></td><td align="center" rowspan="1" colspan="1"><italic>A</italic> ≫ <italic>B</italic> </td></tr><tr><td align="left" rowspan="1" colspan="1"> 0.2</td><td align="center" rowspan="1" colspan="1"> 98.9</td><td align="center" rowspan="1" colspan="1"><italic>*Reg(C:Phy(T:A), T:B)</italic></td><td align="center" rowspan="1" colspan="1"><italic>A</italic> ≫ <italic>B</italic></td></tr><tr><td align="left" rowspan="1" colspan="1"> 0.2</td><td align="center" rowspan="1" colspan="1"> 99.1</td><td align="center" rowspan="1" colspan="1"><italic>*Reg(C:Phy(T:A), T:Phy(T:B))</italic></td><td align="center" rowspan="1" colspan="1"><italic>A</italic> ≫ <italic>B</italic></td></tr></tbody></table></table-wrap><table-wrap id="tab3" position="float"><label>Table 3</label><caption><p>Indirect associations between gene <italic>A</italic> and gene <italic>B</italic>, established by combining binding and regulatory events through a common interaction partner gene <italic>Z</italic>. Bindings are represented with × and for regulations <italic>A</italic> > <italic>B</italic> means <italic>A</italic> regulates <italic>B</italic>. </p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1"> Association</th><th align="center" rowspan="1" colspan="1"> Interpretation</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><italic>A</italic> > <italic>Z</italic> < <italic>B</italic></td><td align="center" rowspan="1" colspan="1"><italic>A</italic> and <italic>B</italic> coregulate <italic>Z</italic></td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>A</italic> < <italic>Z</italic> > <italic>B</italic></td><td align="center" rowspan="1" colspan="1"><italic>A</italic> and <italic>B</italic> are being regulated by <italic>Z</italic></td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>A</italic> × <italic>Z</italic> × <italic>B</italic></td><td align="center" rowspan="1" colspan="1"><italic>A</italic> and <italic>B</italic> share a common binding partner <italic>Z</italic></td></tr></tbody></table></table-wrap><table-wrap id="tab4" position="float"><label>Table 4</label><caption><p>Gene symbol coverage comparison, showing the number of distinct canonical symbols as well as the number of different occurrences covered, out of the total number of 40.3 M extracted gene symbols. </p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1"></th><th align="center" colspan="2" rowspan="1"> Distinct symbols</th><th align="center" colspan="2" rowspan="1"> Occurrences</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"> Canonical</td><td align="center" rowspan="1" colspan="1"> 1833.1 K</td><td align="center" rowspan="1" colspan="1"> 100.0%</td><td align="center" rowspan="1" colspan="1"> 40.3 M</td><td align="center" rowspan="1" colspan="1"> 100.0%</td></tr><tr><td align="left" rowspan="1" colspan="1"> HomoloGene</td><td align="center" rowspan="1" colspan="1"> 68.2 K</td><td align="center" rowspan="1" colspan="1"> 3.7%</td><td align="center" rowspan="1" colspan="1"> 21.1 M</td><td align="center" rowspan="1" colspan="1"> 52.3%</td></tr><tr><td align="left" rowspan="1" colspan="1"> Ensembl</td><td align="center" rowspan="1" colspan="1"> 60.0 K</td><td align="center" rowspan="1" colspan="1"> 3.2%</td><td align="center" rowspan="1" colspan="1"> 20.9 M</td><td align="center" rowspan="1" colspan="1"> 51.8%</td></tr><tr><td align="left" rowspan="1" colspan="1"> Ensembl Genomes</td><td align="center" rowspan="1" colspan="1"> 100.6 K</td><td align="center" rowspan="1" colspan="1"> 5.5%</td><td align="center" rowspan="1" colspan="1"> 24.3 M</td><td align="center" rowspan="1" colspan="1"> 60.1%</td></tr></tbody></table></table-wrap></floats-group></pmc><affiliations><list><country><li>Belgique</li><li>Finlande</li></country><region><li>Finlande occidentale</li></region><settlement><li>Turku</li></settlement><orgName><li>Université de Turku</li></orgName></list><tree><country name="Belgique"><noRegion><name sortKey="Van Landeghem, Sofie" sort="Van Landeghem, Sofie" uniqKey="Van Landeghem S" first="Sofie" last="Van Landeghem">Sofie Van Landeghem</name></noRegion><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><name sortKey="Van Landeghem, Sofie" sort="Van Landeghem, Sofie" uniqKey="Van Landeghem S" first="Sofie" last="Van Landeghem">Sofie Van Landeghem</name></country><country name="Finlande"><region name="Finlande occidentale"><name sortKey="Hakala, Kai" sort="Hakala, Kai" uniqKey="Hakala K" first="Kai" last="Hakala">Kai Hakala</name></region><name sortKey="Ginter, Filip" sort="Ginter, Filip" uniqKey="Ginter F" first="Filip" last="Ginter">Filip Ginter</name><name sortKey="Ronnqvist, Samuel" sort="Ronnqvist, Samuel" uniqKey="Ronnqvist S" first="Samuel" last="Rönnqvist">Samuel Rönnqvist</name><name sortKey="Salakoski, Tapio" sort="Salakoski, Tapio" uniqKey="Salakoski T" first="Tapio" last="Salakoski">Tapio Salakoski</name><name sortKey="Salakoski, Tapio" sort="Salakoski, Tapio" uniqKey="Salakoski T" first="Tapio" last="Salakoski">Tapio Salakoski</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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