Figure Text Extraction in Biomedical Literature
Identifieur interne : 000377 ( Main/Merge ); précédent : 000376; suivant : 000378Figure Text Extraction in Biomedical Literature
Auteurs : Daehyun Kim ; Hong YuSource :
- PLoS ONE [ 1932-6203 ] ; 2011.
English descriptors
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Abstract
Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (
We first evaluated an off-the-shelf Optical Character Recognition (OCR) tool on its ability to extract text from figures appearing in biomedical full-text articles. We then developed a Figure Text Extraction Tool (FigTExT) to improve the performance of the OCR tool for figure text extraction through the use of three innovative components:
The evaluation on 382
Url:
DOI: 10.1371/journal.pone.0015338
PubMed: 21249186
PubMed Central: 3020938
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Figure Text Extraction in Biomedical Literature</title><author><name sortKey="Kim, Daehyun" sort="Kim, Daehyun" uniqKey="Kim D" first="Daehyun" last="Kim">Daehyun Kim</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Yu, Hong" sort="Yu, Hong" uniqKey="Yu H" first="Hong" last="Yu">Hong Yu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21249186</idno><idno type="pmc">3020938</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020938</idno><idno type="RBID">PMC:3020938</idno><idno type="doi">10.1371/journal.pone.0015338</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000185</idno><idno type="wicri:Area/Pmc/Curation">000185</idno><idno type="wicri:Area/Pmc/Checkpoint">000129</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000037</idno><idno type="wicri:Area/PubMed/Curation">000037</idno><idno type="wicri:Area/PubMed/Checkpoint">000037</idno><idno type="wicri:Area/Ncbi/Merge">000096</idno><idno type="wicri:Area/Ncbi/Curation">000096</idno><idno type="wicri:Area/Ncbi/Checkpoint">000096</idno><idno type="wicri:Area/Main/Merge">000377</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Figure Text Extraction in Biomedical Literature</title><author><name sortKey="Kim, Daehyun" sort="Kim, Daehyun" uniqKey="Kim D" first="Daehyun" last="Kim">Daehyun Kim</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Yu, Hong" sort="Yu, Hong" uniqKey="Yu H" first="Hong" last="Yu">Hong Yu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology</term><term>Computer Graphics</term><term>Data Mining</term><term>Information Storage and Retrieval (methods)</term><term>Information Storage and Retrieval (standards)</term><term>Internet</term><term>Pattern Recognition, Automated (methods)</term><term>Pattern Recognition, Automated (standards)</term><term>Periodicals as Topic</term><term>PubMed</term><term>Software</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Information Storage and Retrieval</term><term>Pattern Recognition, Automated</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Information Storage and Retrieval</term><term>Pattern Recognition, Automated</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Computer Graphics</term><term>Data Mining</term><term>Internet</term><term>Periodicals as Topic</term><term>PubMed</term><term>Software</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (<ext-link ext-link-type="uri" xlink:href="http://figuresearch.askHERMES.org">http://figuresearch.askHERMES.org</ext-link>) to allow bioscientists to access figures efficiently. Since text frequently appears in figures, automatically extracting such text may assist the task of mining information from figures. Little research, however, has been conducted exploring text extraction from biomedical figures.</p></sec><sec><title>Methodology</title><p>We first evaluated an off-the-shelf Optical Character Recognition (OCR) tool on its ability to extract text from figures appearing in biomedical full-text articles. We then developed a Figure Text Extraction Tool (FigTExT) to improve the performance of the OCR tool for figure text extraction through the use of three innovative components: <italic>image preprocessing</italic>, <italic>character recognition</italic>, and <italic>text correction</italic>. We first developed <italic>image preprocessing</italic> to enhance image quality and to improve text localization. Then we adapted the off-the-shelf OCR tool on the improved text localization for <italic>character recognition</italic>. Finally, we developed and evaluated a novel <italic>text correction</italic> framework by taking advantage of figure-specific lexicons.</p></sec><sec><title>Results/Conclusions</title><p>The evaluation on 382 <xref ref-type="fig" rid="pone-0015338-g009">figures (9</xref>,643 figure texts in total) randomly selected from PubMed Central full-text articles shows that FigTExT performed with 84% precision, 98% recall, and 90% F1-score for text localization and with 62.5% precision, 51.0% recall and 56.2% F1-score for figure text extraction. When limiting figure texts to those judged by domain experts to be important content, FigTExT performed with 87.3% precision, 68.8% recall, and 77% F1-score. FigTExT significantly improved the performance of the off-the-shelf OCR tool we used, which on its own performed with 36.6% precision, 19.3% recall, and 25.3% F1-score for text extraction. In addition, our results show that FigTExT can extract texts that do not appear in figure captions or other associated text, further suggesting the potential utility of FigTExT for improving figure search.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Shatkay, H" uniqKey="Shatkay H">H Shatkay</name></author><author><name sortKey="Chen, N" uniqKey="Chen N">N Chen</name></author><author><name sortKey="Blostein, D" uniqKey="Blostein D">D Blostein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rafkind, B" uniqKey="Rafkind B">B Rafkind</name></author><author><name sortKey="Lee, M" uniqKey="Lee M">M Lee</name></author><author><name sortKey="Chang, Sf" uniqKey="Chang S">SF Chang</name></author><author><name sortKey="Yu, H" uniqKey="Yu H">H Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, H" uniqKey="Yu H">H Yu</name></author><author><name sortKey="Lee, M" uniqKey="Lee M">M Lee</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, H" uniqKey="Guturu H">H Guturu</name></author><author><name sortKey="Ksikes, A" uniqKey="Ksikes A">A Ksikes</name></author><author><name sortKey="Nakov, P" uniqKey="Nakov P">P Nakov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kahn, Ce" uniqKey="Kahn C">CE Kahn</name></author><author><name sortKey="Thao, C" uniqKey="Thao C">C Thao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qian, Y" uniqKey="Qian Y">Y Qian</name></author><author><name sortKey="Murphy, Rf" uniqKey="Murphy R">RF Murphy</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="Ahmed, A" uniqKey="Ahmed A">A Ahmed</name></author><author><name sortKey="Xing, Ep" uniqKey="Xing E">EP Xing</name></author><author><name sortKey="Cohen, Ww" uniqKey="Cohen W">WW Cohen</name></author><author><name sortKey="Murphy, Rf" uniqKey="Murphy R">RF Murphy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Murphy, Rf" uniqKey="Murphy R">RF Murphy</name></author><author><name sortKey="Velliste, M" uniqKey="Velliste M">M Velliste</name></author><author><name sortKey="Yao, J" uniqKey="Yao J">J Yao</name></author><author><name sortKey="Porreca, G" uniqKey="Porreca G">G Porreca</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, H" uniqKey="Yu H">H Yu</name></author><author><name sortKey="Lee, M" uniqKey="Lee M">M Lee</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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, H" uniqKey="Yu H">H Yu</name></author><author><name sortKey="Agarwal, S" uniqKey="Agarwal S">S Agarwal</name></author><author><name sortKey="Johnston, M" uniqKey="Johnston M">M Johnston</name></author><author><name sortKey="Cohen, A" uniqKey="Cohen A">A Cohen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, H" uniqKey="Yu H">H Yu</name></author><author><name sortKey="Liu, F" uniqKey="Liu F">F Liu</name></author><author><name sortKey="Ramesh, Bp" uniqKey="Ramesh B">BP Ramesh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shatkay, H" uniqKey="Shatkay H">H Shatkay</name></author><author><name sortKey="Pan, F" uniqKey="Pan F">F Pan</name></author><author><name sortKey="Rzhetsky, A" uniqKey="Rzhetsky A">A Rzhetsky</name></author><author><name sortKey="Wilbur, Wj" uniqKey="Wilbur W">WJ Wilbur</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, D" uniqKey="Kim D">D Kim</name></author><author><name sortKey="Yu, H" uniqKey="Yu H">H Yu</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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Z" uniqKey="Liu Z">Z Liu</name></author><author><name sortKey="Sarkar, S" uniqKey="Sarkar S">S Sarkar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, D" uniqKey="Chen D">D Chen</name></author><author><name sortKey="Odobez, J" uniqKey="Odobez J">J Odobez</name></author><author><name sortKey="Thiran, J" uniqKey="Thiran J">J Thiran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gatos, B" uniqKey="Gatos B">B Gatos</name></author><author><name sortKey="Pratikakis, I" uniqKey="Pratikakis I">I Pratikakis</name></author><author><name sortKey="Perantonis, Sj" uniqKey="Perantonis S">SJ Perantonis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, D" uniqKey="Chen D">D Chen</name></author><author><name sortKey="Odobez, J" uniqKey="Odobez J">J Odobez</name></author><author><name sortKey="Bourlard, H" uniqKey="Bourlard H">H Bourlard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Anthimopoulos, M" uniqKey="Anthimopoulos M">M Anthimopoulos</name></author><author><name sortKey="Gatos, B" uniqKey="Gatos B">B Gatos</name></author><author><name sortKey="Pratikakis, I" uniqKey="Pratikakis I">I Pratikakis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Dh" uniqKey="Kim D">DH Kim</name></author><author><name sortKey="Sohn, K" uniqKey="Sohn K">K Sohn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shivakumara, P" uniqKey="Shivakumara P">P Shivakumara</name></author><author><name sortKey="Huang, W" uniqKey="Huang W">W Huang</name></author><author><name sortKey="Tan, Cl" uniqKey="Tan C">CL Tan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kou, Z" uniqKey="Kou Z">Z Kou</name></author><author><name sortKey="Cohen, Ww" uniqKey="Cohen W">WW Cohen</name></author><author><name sortKey="Murphy, Rf" uniqKey="Murphy R">RF Murphy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gonzalez, R" uniqKey="Gonzalez R">R Gonzalez</name></author><author><name sortKey="Woods, R" uniqKey="Woods R">R Woods</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hsieh, H" uniqKey="Hsieh H">H Hsieh</name></author><author><name sortKey="Andrew, H" uniqKey="Andrew H">H Andrew</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name></author><author><name sortKey="Yang, J" uniqKey="Yang J">J Yang</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Waibel, A" uniqKey="Waibel A">A Waibel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name></author><author><name sortKey="Yuille, Al" uniqKey="Yuille A">AL Yuille</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weinman, Jj" uniqKey="Weinman J">JJ Weinman</name></author><author><name sortKey="Learned Miller, E" uniqKey="Learned Miller E">E Learned-Miller</name></author><author><name sortKey="Hanson, A" uniqKey="Hanson A">A Hanson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Damerau, Fj" uniqKey="Damerau F">FJ Damerau</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wagner, Ra" uniqKey="Wagner R">RA Wagner</name></author><author><name sortKey="Michael, Jf" uniqKey="Michael J">JF Michael</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Riseman, Em" uniqKey="Riseman E">EM Riseman</name></author><author><name sortKey="Hanson, Ar" uniqKey="Hanson A">AR Hanson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zamora, Em" uniqKey="Zamora E">EM Zamora</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kashyap, Rl" uniqKey="Kashyap R">RL Kashyap</name></author><author><name sortKey="Oommen, J" uniqKey="Oommen J">J Oommen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hodge, V" uniqKey="Hodge V">V Hodge</name></author><author><name sortKey="Jim, A" uniqKey="Jim A">A Jim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lucas, Sm" uniqKey="Lucas S">SM Lucas</name></author><author><name sortKey="Patoulas, G" uniqKey="Patoulas G">G Patoulas</name></author><author><name sortKey="Downton, Ac" uniqKey="Downton A">AC Downton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schambach, Mp" uniqKey="Schambach M">MP Schambach</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruch, P" uniqKey="Ruch P">P Ruch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, M" uniqKey="Li M">M Li</name></author><author><name sortKey="Yang, Z" uniqKey="Yang Z">Z Yang</name></author><author><name sortKey="Muhua, Z" uniqKey="Muhua Z">Z Muhua</name></author><author><name sortKey="Ming, Z" uniqKey="Ming Z">Z Ming</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ringlstetter, C" uniqKey="Ringlstetter C">C Ringlstetter</name></author><author><name sortKey="K, Us" uniqKey="K U">US K</name></author><author><name sortKey="Stoyan, M" uniqKey="Stoyan M">M Stoyan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Donoser, M" uniqKey="Donoser M">M Donoser</name></author><author><name sortKey="Bischof, H" uniqKey="Bischof H">H Bischof</name></author><author><name sortKey="Wagner, S" uniqKey="Wagner S">S Wagner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tong, X" uniqKey="Tong X">X Tong</name></author><author><name sortKey="Evans, Da" uniqKey="Evans D">DA Evans</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thillou, C" uniqKey="Thillou C">C Thillou</name></author><author><name sortKey="Ferreira, S" uniqKey="Ferreira S">S Ferreira</name></author><author><name sortKey="Gosselin, B" uniqKey="Gosselin B">B Gosselin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stehouwer, H" uniqKey="Stehouwer H">H Stehouwer</name></author><author><name sortKey="Zaanen, M" uniqKey="Zaanen M">M Zaanen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jones, Mp" uniqKey="Jones M">MP Jones</name></author><author><name sortKey="James, Hm" uniqKey="James H">HM James</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martins, B" uniqKey="Martins B">B Martins</name></author><author><name sortKey="Mario, Js" uniqKey="Mario J">JS Mário</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Levenshtein, Vi" uniqKey="Levenshtein V">VI Levenshtein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paterson, M" uniqKey="Paterson M">M Paterson</name></author><author><name sortKey="Dancik, V" uniqKey="Dancik V">V Dancik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thompson, Jd" uniqKey="Thompson J">JD Thompson</name></author><author><name sortKey="Higgins, Dg" uniqKey="Higgins D">DG Higgins</name></author><author><name sortKey="Gibson, Tj" uniqKey="Gibson T">TJ Gibson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Glasner, D" uniqKey="Glasner D">D Glasner</name></author><author><name sortKey="Bagon, S" uniqKey="Bagon S">S Bagon</name></author><author><name sortKey="Irani, M" uniqKey="Irani M">M Irani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fattal, R" uniqKey="Fattal R">R Fattal</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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