Annotated Chemical Patent Corpus: A Gold Standard for Text Mining
Identifieur interne : 000110 ( Main/Exploration ); précédent : 000109; suivant : 000111Annotated Chemical Patent Corpus: A Gold Standard for Text Mining
Auteurs : Saber A. Akhondi [Pays-Bas] ; Alexander G. Klenner [Allemagne] ; Christian Tyrchan [Suède] ; Anil K. Manchala [Inde] ; Kiran Boppana [Inde] ; Daniel Lowe [Royaume-Uni] ; Marc Zimmermann [Allemagne] ; Sarma A. R. P. Jagarlapudi [Inde] ; Roger Sayle [Royaume-Uni] ; Jan A. Kors [Pays-Bas] ; Sorel Muresan [Suède]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at
Url:
DOI: 10.1371/journal.pone.0107477
PubMed: 25268232
PubMed Central: 4182036
Affiliations:
- Allemagne, Inde, Pays-Bas, Royaume-Uni, Suède
- Angleterre, District de Cologne, Hollande-Méridionale, Rhénanie-du-Nord-Westphalie
- Rotterdam, Sankt Augustin
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000014
- to stream Pmc, to step Curation: 000014
- to stream Pmc, to step Checkpoint: 000057
- to stream Ncbi, to step Merge: 000211
- to stream Ncbi, to step Curation: 000211
- to stream Ncbi, to step Checkpoint: 000211
- to stream Main, to step Merge: 000111
- to stream Main, to step Curation: 000110
Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at <ext-link ext-link-type="uri" xlink:href="http://www.biosemantics.org">www.biosemantics.org</ext-link>
.</p>
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</author>
<author><name sortKey="Mandel, M" uniqKey="Mandel M">M Mandel</name>
</author>
<author><name sortKey="Mcdonald, R" uniqKey="Mcdonald R">R McDonald</name>
</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Kolarik, C" uniqKey="Kolarik C">C Kolárik</name>
</author>
<author><name sortKey="Klinger, R" uniqKey="Klinger R">R Klinger</name>
</author>
<author><name sortKey="Friedrich, Cm" uniqKey="Friedrich C">CM Friedrich</name>
</author>
<author><name sortKey="Hofmann Apitius, M" uniqKey="Hofmann Apitius M">M Hofmann-Apitius</name>
</author>
<author><name sortKey="Fluck, J" uniqKey="Fluck J">J Fluck</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Krallinger, M" uniqKey="Krallinger M">M Krallinger</name>
</author>
<author><name sortKey="Leitner, F" uniqKey="Leitner F">F Leitner</name>
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<author><name sortKey="Vazquez, M" uniqKey="Vazquez M">M Vazquez</name>
</author>
<author><name sortKey="Oyarzabal, J" uniqKey="Oyarzabal J">J Oyarzabal</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Grego, T" uniqKey="Grego T">T Grego</name>
</author>
<author><name sortKey="P Zik, P" uniqKey="P Zik P">P Pęzik</name>
</author>
<author><name sortKey="Couto, Fm" uniqKey="Couto F">FM Couto</name>
</author>
<author><name sortKey="Rebholz Schuhmann, D" uniqKey="Rebholz Schuhmann D">D Rebholz-Schuhmann</name>
</author>
</analytic>
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</author>
<author><name sortKey="De Matos, P" uniqKey="De Matos P">P De Matos</name>
</author>
<author><name sortKey="Ennis, M" uniqKey="Ennis M">M Ennis</name>
</author>
<author><name sortKey="Hastings, J" uniqKey="Hastings J">J Hastings</name>
</author>
<author><name sortKey="Zbinden, M" uniqKey="Zbinden M">M Zbinden</name>
</author>
</analytic>
</biblStruct>
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</author>
<author><name sortKey="Alcantara, R" uniqKey="Alcantara R">R Alcántara</name>
</author>
<author><name sortKey="Dekker, A" uniqKey="Dekker A">A Dekker</name>
</author>
<author><name sortKey="Ennis, M" uniqKey="Ennis M">M Ennis</name>
</author>
<author><name sortKey="Hastings, J" uniqKey="Hastings J">J Hastings</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Sayle, R" uniqKey="Sayle R">R Sayle</name>
</author>
<author><name sortKey="Xie, Ph" uniqKey="Xie P">PH Xie</name>
</author>
<author><name sortKey="Muresan, S" uniqKey="Muresan S">S Muresan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Akhondi, Sa" uniqKey="Akhondi S">SA Akhondi</name>
</author>
<author><name sortKey="Kors, Ja" uniqKey="Kors J">JA Kors</name>
</author>
<author><name sortKey="Muresan, S" uniqKey="Muresan S">S Muresan</name>
</author>
</analytic>
</biblStruct>
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</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Heller, S" uniqKey="Heller S">S Heller</name>
</author>
<author><name sortKey="Mcnaught, A" uniqKey="Mcnaught A">A McNaught</name>
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<author><name sortKey="Stein, S" uniqKey="Stein S">S Stein</name>
</author>
<author><name sortKey="Tchekhovskoi, D" uniqKey="Tchekhovskoi D">D Tchekhovskoi</name>
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<author><name sortKey="Pletnev, I" uniqKey="Pletnev I">I Pletnev</name>
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</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Lowe, Dm" uniqKey="Lowe D">DM Lowe</name>
</author>
<author><name sortKey="Sayle, Ra" uniqKey="Sayle R">RA Sayle</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stenetorp, P" uniqKey="Stenetorp P">P Stenetorp</name>
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</analytic>
</biblStruct>
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</div1>
</back>
</TEI>
<affiliations><list><country><li>Allemagne</li>
<li>Inde</li>
<li>Pays-Bas</li>
<li>Royaume-Uni</li>
<li>Suède</li>
</country>
<region><li>Angleterre</li>
<li>District de Cologne</li>
<li>Hollande-Méridionale</li>
<li>Rhénanie-du-Nord-Westphalie</li>
</region>
<settlement><li>Rotterdam</li>
<li>Sankt Augustin</li>
</settlement>
</list>
<tree><country name="Pays-Bas"><region name="Hollande-Méridionale"><name sortKey="Akhondi, Saber A" sort="Akhondi, Saber A" uniqKey="Akhondi S" first="Saber A." last="Akhondi">Saber A. Akhondi</name>
</region>
<name sortKey="Kors, Jan A" sort="Kors, Jan A" uniqKey="Kors J" first="Jan A." last="Kors">Jan A. Kors</name>
</country>
<country name="Allemagne"><region name="Rhénanie-du-Nord-Westphalie"><name sortKey="Klenner, Alexander G" sort="Klenner, Alexander G" uniqKey="Klenner A" first="Alexander G." last="Klenner">Alexander G. Klenner</name>
</region>
<name sortKey="Zimmermann, Marc" sort="Zimmermann, Marc" uniqKey="Zimmermann M" first="Marc" last="Zimmermann">Marc Zimmermann</name>
</country>
<country name="Suède"><noRegion><name sortKey="Tyrchan, Christian" sort="Tyrchan, Christian" uniqKey="Tyrchan C" first="Christian" last="Tyrchan">Christian Tyrchan</name>
</noRegion>
<name sortKey="Muresan, Sorel" sort="Muresan, Sorel" uniqKey="Muresan S" first="Sorel" last="Muresan">Sorel Muresan</name>
</country>
<country name="Inde"><noRegion><name sortKey="Manchala, Anil K" sort="Manchala, Anil K" uniqKey="Manchala A" first="Anil K." last="Manchala">Anil K. Manchala</name>
</noRegion>
<name sortKey="Boppana, Kiran" sort="Boppana, Kiran" uniqKey="Boppana K" first="Kiran" last="Boppana">Kiran Boppana</name>
<name sortKey="Jagarlapudi, Sarma A R P" sort="Jagarlapudi, Sarma A R P" uniqKey="Jagarlapudi S" first="Sarma A. R. P." last="Jagarlapudi">Sarma A. R. P. Jagarlapudi</name>
</country>
<country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Lowe, Daniel" sort="Lowe, Daniel" uniqKey="Lowe D" first="Daniel" last="Lowe">Daniel Lowe</name>
</region>
<name sortKey="Sayle, Roger" sort="Sayle, Roger" uniqKey="Sayle R" first="Roger" last="Sayle">Roger Sayle</name>
</country>
</tree>
</affiliations>
</record>
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