en:news:challenges:biocreative-v:track-2-chemdner
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en:news:challenges:biocreative-v:track-2-chemdner [2017/04/20 12:19] pzczxs 创建 |
en:news:challenges:biocreative-v:track-2-chemdner [2017/04/20 12:27] (当前版本) pzczxs [Timeline] |
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| ====Timeline==== | ====Timeline==== | ||
| *January 2015: Task announcement & call for participation | *January 2015: Task announcement & call for participation | ||
| - | *March 2nd: Sample set patent abstract plain text release: {{:news:challenge:biocreative-v:chemdner_sample_text.zip|CHEMDNER-patents sample text}} | + | *March 2nd: Sample set patent abstract plain text release: {{resources:datasets:chemdner_sample_text.zip|CHEMDNER-patents sample text}} |
| - | *March 27th: Sample set annotation release: {{:news:challenge:biocreative-v:chemdner_cpd_sample.zip|CPD subtask}}, {{:news:challenge:biocreative-v:chemdner_cemp_sample_v02.zip|CEMP subtask}} (corrected, version 2), {{:news:challenge:biocreative-v:chemdner_cer_sample.zip|CER subtask}} | + | *March 27th: Sample set annotation release: {{resources:datasets:chemdner_cpd_sample.zip|CPD subtask}}, {{resources:datasets:chemdner_cemp_sample_v02.zip|CEMP subtask}} (corrected, version 2), {{resources:datasets:chemdner_cer_sample.zip|CER subtask}} |
| *End April 2015: Release of training data with annotation guidelines | *End April 2015: Release of training data with annotation guidelines | ||
| *End May 2015: Release of development data | *End May 2015: Release of development data | ||
| 行 72: | 行 72: | ||
| ====References==== | ====References==== | ||
| - | -Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Jelen Oyarzabal, and Alfonso Valencia, 2015. [[http://www.jcheminf.com/content/7/S1/S1/abstract|CHEMDNER: The Drugs and Chemical Names Extraction Challenge]]. //Journal of Cheminformatics//, Vol. 7, No. Suppl 1, pp. S1. ''{{news:challenge:klrv_15.pdf|PDF}}'' | + | -Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Jelen Oyarzabal, and Alfonso Valencia, 2015. [[http://www.jcheminf.com/content/7/S1/S1/abstract|CHEMDNER: The Drugs and Chemical Names Extraction Challenge]]. //Journal of Cheminformatics//, Vol. 7, No. Suppl 1, pp. S1. ''{{resources:papers:klrv_15.pdf|PDF}}'' |
| - | -Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, and Alfonso Valencia, 2013. [[http://www.biocreative.org/media/store/files/2013/bc4_v2_1.pdf|Overview of the Chemical Compound and Drug Name Recognition (CHEMDNER) Task]]. In: Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, and Alfonso Valencia (eds) //Proceedings of the 4th BioCreative Challenge Evaluation Workshop//, Vol. 2,, Vol. 2, pp. 2-33. ''{{news:challenge:klrv_13.pdf|PDF}}'' | + | -Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, and Alfonso Valencia, 2013. [[http://www.biocreative.org/media/store/files/2013/bc4_v2_1.pdf|Overview of the Chemical Compound and Drug Name Recognition (CHEMDNER) Task]]. In: Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, and Alfonso Valencia (eds) //Proceedings of the 4th BioCreative Challenge Evaluation Workshop//, Vol. 2,, Vol. 2, pp. 2-33. ''{{resources:papers:klrv_13.pdf|PDF}}'' |
| - | -Tiago Grego, Piotr Pęzik, Francisco M. Couto, and Dietrich Rebholz-Schuhmann, 2009. [[http://link.springer.com/chapter/10.1007/978-3-642-02481-8_144|Identification of chemical entities in patent documents]]. In: //Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living//, pp. 942-949, Springer Berlin Heidelberg. ''{{news:challenge:gpcr-s09.pdf|PDF}}'' | + | -Tiago Grego, Piotr Pęzik, Francisco M. Couto, and Dietrich Rebholz-Schuhmann, 2009. [[http://link.springer.com/chapter/10.1007/978-3-642-02481-8_144|Identification of chemical entities in patent documents]]. In: //Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living//, pp. 942-949, Springer Berlin Heidelberg. ''{{resources:papers:gpcr-s09.pdf|PDF}}'' |
| - | -David M. Jessop, Sam E. Adams, and Peter Murray-Rust, 2011. [[http://www.jcheminf.com/content/3/1/40|Mining Chemical Information from Open Patents]]. //Journal of cheminformatics//, Vol. 3, No. 1, pp. 40. ''{{news:challenge:jam-r11.pdf|PDF}}'' | + | -David M. Jessop, Sam E. Adams, and Peter Murray-Rust, 2011. [[http://www.jcheminf.com/content/3/1/40|Mining Chemical Information from Open Patents]]. //Journal of cheminformatics//, Vol. 3, No. 1, pp. 40. ''{{resources:papers:jam-r11.pdf|PDF}}'' |
| - | -Harsha Gurulingappa, Bernd Müller, Roman Klinger, Heinz-Theodor Mevissen, Martin Hofmann-Apitius, Christoph M. Friedrich, and Juliance Fluck, 2010. [[http://trec.nist.gov/pubs/trec19/papers/fraunhofer-scai.chem.rev.pdf|Prior Art Search in Chemistry Patents Based On Semantic Concepts and Co-Citation Analysis]]. In: //Proceedings of the 19th Text REtrieval Conference (TREC)//. ''{{news:challenge:gmkm_10.pdf|PDF}}'' | + | -Harsha Gurulingappa, Bernd Müller, Roman Klinger, Heinz-Theodor Mevissen, Martin Hofmann-Apitius, Christoph M. Friedrich, and Juliance Fluck, 2010. [[http://trec.nist.gov/pubs/trec19/papers/fraunhofer-scai.chem.rev.pdf|Prior Art Search in Chemistry Patents Based On Semantic Concepts and Co-Citation Analysis]]. In: //Proceedings of the 19th Text REtrieval Conference (TREC)//. ''{{resources:papers:gmkm_10.pdf|PDF}}'' |
| - | -Roman Klinger, Corinna Kolarik, Juliane Fluck, Martin Hofmann-Apitius, and Christoph M. Friedrich, 2008. [[http://bioinformatics.oxfordjournals.org/content/24/13/i268.full|Detection of IUPAC and IUPAC-Like Chemical Names]]. //Bioinformatics//, Vol. 24, No. 13, pp. i268-i276. ''{{news:challenge:kkfh-a_08.pdf|PDF}}'' | + | -Roman Klinger, Corinna Kolarik, Juliane Fluck, Martin Hofmann-Apitius, and Christoph M. Friedrich, 2008. [[http://bioinformatics.oxfordjournals.org/content/24/13/i268.full|Detection of IUPAC and IUPAC-Like Chemical Names]]. //Bioinformatics//, Vol. 24, No. 13, pp. i268-i276. ''{{resources:papers:kkfh-a_08.pdf|PDF}}'' |
| - | -Peter Corbett and Ann Copestake, 2008. [[http://www.biomedcentral.com/1471-2105/9/S11/S4|Cascaded Classifiers for Confidence-Based Chemical Named Entity Recognition]]. //BMC Bioinformatics//, Vol. 9, No. Suppl 11, pp. S4. ''{{news:challenge:cc08.pdf|PDF}}'' | + | -Peter Corbett and Ann Copestake, 2008. [[http://www.biomedcentral.com/1471-2105/9/S11/S4|Cascaded Classifiers for Confidence-Based Chemical Named Entity Recognition]]. //BMC Bioinformatics//, Vol. 9, No. Suppl 11, pp. S4. ''{{resources:papers:cc08.pdf|PDF}}'' |
| ===Corpus==== | ===Corpus==== | ||
| - | -Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe, Roger A Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sergio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V Ramanan, Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A Akhondi, Jan A Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Komandur Elayavilli Ravikumar, Andre Lamurias, Francisco M Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Joaquim Cruz, Isabel Segura-Bedmar, Paloma Martinez, Julen Oyarzabal, and Alfonso Valencia, 2015. [[http://www.jcheminf.com/content/7/S1/S2/abstract|The CHEMDNER Corpus of Chemicals and Drugs and its Annotation Principles]]. //Journal of Cheminformatics//, Vol. 7, No. Suppl 1, pp. S2. ''{{zh:people:xush:papers:krl_15.pdf|PDF}}'' | + | -Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe, Roger A Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sergio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V Ramanan, Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A Akhondi, Jan A Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Komandur Elayavilli Ravikumar, Andre Lamurias, Francisco M Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Joaquim Cruz, Isabel Segura-Bedmar, Paloma Martinez, Julen Oyarzabal, and Alfonso Valencia, 2015. [[http://www.jcheminf.com/content/7/S1/S2/abstract|The CHEMDNER Corpus of Chemicals and Drugs and its Annotation Principles]]. //Journal of Cheminformatics//, Vol. 7, No. Suppl 1, pp. S2. ''{{xushuo:papers:krl_15.pdf|PDF}}'' |
| - | -Saber A. Akhondi, Alexander G. Klenner, Christian Tyrchan, Anil K. Manchala, Kiran Boppana, Daniel Lowe, Marc Zimmermann, Sarma A. R. P. Jagarlapudi, Roger Sayle, Jan A. Kors, and Sorel Muresan, 2014. [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107477|Annotated Chemical Patent Corpus: A Gold Standard for Text Mining]]. //PloS one//, Vol. 9, No. 9, pp. e107477. ''{{news:challenge:aktm_14.pdf|PDF}}'' ''{{group:datasets:patent_corpus.zip|data}}'' | + | -Saber A. Akhondi, Alexander G. Klenner, Christian Tyrchan, Anil K. Manchala, Kiran Boppana, Daniel Lowe, Marc Zimmermann, Sarma A. R. P. Jagarlapudi, Roger Sayle, Jan A. Kors, and Sorel Muresan, 2014. [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107477|Annotated Chemical Patent Corpus: A Gold Standard for Text Mining]]. //PloS one//, Vol. 9, No. 9, pp. e107477. ''{{resources:papers:aktm_14.pdf|PDF}}'' ''{{resources:datasets:patent_corpus.zip|data}}'' |
| - | -Márton Kiss, Ágoston Nagy, Veronika Vincze, Attila Almási, Zoltán Alexin, and János Csirik, 2012. A Manually Annotated Corpus of Pharmaceutical Patents. //Text, Speech and Dialogue//. Springer Berlin Heidelberg. pp. 135–142. ''{{news:challenge:knva_12.pdf|PDF}}'' | + | -Márton Kiss, Ágoston Nagy, Veronika Vincze, Attila Almási, Zoltán Alexin, and János Csirik, 2012. A Manually Annotated Corpus of Pharmaceutical Patents. //Text, Speech and Dialogue//. Springer Berlin Heidelberg. pp. 135–142. ''{{resources:papers:knva_12.pdf|PDF}}'' |
| ===Domain Resource=== | ===Domain Resource=== | ||
| - | -David S. Wishart, Craig Knox, An Chi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, and Jennifer Woolsey, 2006. [[http://nar.oxfordjournals.org/content/34/suppl_1/D668.long|DrugBank: A Comprehensive Resource for in silico Drug Discovery and Exploration]]. //Nucleic Acids Research//, Vol. 34, No. suppl 1, pp. D668-D672. ''{{news:challenge:wkgs_06.pdf|PDF}}'' ''{{http://www.drugbank.ca/downloads|data}}'' | + | -David S. Wishart, Craig Knox, An Chi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, and Jennifer Woolsey, 2006. [[http://nar.oxfordjournals.org/content/34/suppl_1/D668.long|DrugBank: A Comprehensive Resource for in silico Drug Discovery and Exploration]]. //Nucleic Acids Research//, Vol. 34, No. suppl 1, pp. D668-D672. ''{{resources:papers:wkgs_06.pdf|PDF}}'' ''{{http://www.drugbank.ca/downloads|data}}'' |
| - | -Feng Zhu, BuCong Han, Pankaj Kumar, XiangHui Liu, XiaoHua Ma, XiaoNa Wei, Lu Huang, YangFan Guo, LianYi Han, ChanJuan Zheng, and YuZong Chen, 2010. [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808971/|Update of TTD: Therapeutic Target Database]]. //Nucleic Acids Research//, Vol. 38, No. Suppl 1, pp. D787-D791. ''{{news:challenge:zhkl_10.pdf|PDF}}'' | + | -Feng Zhu, BuCong Han, Pankaj Kumar, XiangHui Liu, XiaoHua Ma, XiaoNa Wei, Lu Huang, YangFan Guo, LianYi Han, ChanJuan Zheng, and YuZong Chen, 2010. [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808971/|Update of TTD: Therapeutic Target Database]]. //Nucleic Acids Research//, Vol. 38, No. Suppl 1, pp. D787-D791. ''{{resources:papers:zhkl_10.pdf|PDF}}'' |
| - | -Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcantara, Michael Darsow, Mickael Guedj, and Michael Ashburner, 2007. [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238832/|ChEBI: A Database and Ontology for Chemical Entities of Biological Interest]]. //Nucleic Acids Research//, Vol. 36, No. Database, pp. D344-350. ''{{news:challenge:ddmeh_07.pdf|PDF}}'' ''{{https://www.ebi.ac.uk/chebi/|data}}'' | + | -Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcantara, Michael Darsow, Mickael Guedj, and Michael Ashburner, 2007. [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238832/|ChEBI: A Database and Ontology for Chemical Entities of Biological Interest]]. //Nucleic Acids Research//, Vol. 36, No. Database, pp. D344-350. ''{{resources:papers:ddmeh_07.pdf|PDF}}'' ''{{https://www.ebi.ac.uk/chebi/|data}}'' |
| - | -Kristina M. Hettne, Rob H. Stierum, Martijn J. Schuemie, Peter J. M. Hendriksen, Bob J. A. Schijvenaars, Erik M. van Mulligen, Jos Kleinjans, and Jan A. Kors, 2009. [[http://bioinformatics.oxfordjournals.org/content/25/22/2983.short|A Dictionary to Identify Small Molecules and Drugs in Free Text]]. //Bioinformatics//, Vol. 25, No. 22, pp. 2983-2991. ''{{news:challenge:jochem.pdf|PDF}}'' ''{{http://www.biosemantics.org/index.php/resources/jochem|data}}'' | + | -Kristina M. Hettne, Rob H. Stierum, Martijn J. Schuemie, Peter J. M. Hendriksen, Bob J. A. Schijvenaars, Erik M. van Mulligen, Jos Kleinjans, and Jan A. Kors, 2009. [[http://bioinformatics.oxfordjournals.org/content/25/22/2983.short|A Dictionary to Identify Small Molecules and Drugs in Free Text]]. //Bioinformatics//, Vol. 25, No. 22, pp. 2983-2991. ''{{resources:papers:jochem.pdf|PDF}}'' ''{{http://www.biosemantics.org/index.php/resources/jochem|data}}'' |
| -Drugs@FDA: a database provided by U.S. Food and Drug Administration. ''{{http://www.fda.gov/Drugs/InformationOnDrugs/ucm079750.htm|data}}'' | -Drugs@FDA: a database provided by U.S. Food and Drug Administration. ''{{http://www.fda.gov/Drugs/InformationOnDrugs/ucm079750.htm|data}}'' | ||
| ====Downloads==== | ====Downloads==== | ||
| - | *{{:news:challenge:biocreative-v:chemdner_cemp_sample_v02.zip|chemdner cemp subtask sample version 2}} | + | *{{resources:datasets:chemdner_cemp_sample_v02.zip|chemdner cemp subtask sample version 2}} |
| - | *{{:news:challenge:biocreative-v:chemdner_cer_sample.zip|chemdner cer subtask sample}} | + | *{{resources:datasets:chemdner_cer_sample.zip|chemdner cer subtask sample}} |
| - | *{{:news:challenge:biocreative-v:chemdner_cpd_sample.zip|chemdner cpd subtask sample}} | + | *{{resources:datasets:chemdner_cpd_sample.zip|chemdner cpd subtask sample}} |
| - | *{{:news:challenge:biocreative-v:chemdner_sample_text.zip|Sample patent abstract text}} | + | *{{resources:datasets:chemdner_sample_text.zip|Sample patent abstract text}} |
en/news/challenges/biocreative-v/track-2-chemdner.1492661971.txt.gz · 最后更改: 2017/04/20 12:19 由 pzczxs