Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine
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Qingyu Chen | Zhiyong Lu | Karin M. Verspoor | Hongfang Liu | Ling Luo | Jinfeng Zhang | Hong-Jie Dai | Zehra Melce Hüsünbeyi | Tung Tran | Ramakanth Kavuluru | Yanshan Wang | Donald C. Comeau | Chih-Hsuan Wei | Rezarta Islamaj Dogan | Arzucan Özgür | Berna Altinel | Sun Kim | Andrew Chatr-aryamontri | Albert Steppi | Aris Fergadis | Rui Antunes | Chen-Kai Wang | Jinchan Qu | Zhuang Liu | Nagesh C. Panyam | Aparna Elangovan | Sérgio Matos | K. Verspoor | Hongfang Liu | Hong-Jie Dai | Zhiyong Lu | Chih-Hsuan Wei | Arzucan Özgür | A. Chatr-aryamontri | Jinfeng Zhang | R. Dogan | Qingyu Chen | Sun Kim | Yanshan Wang | Aparna Elangovan | Ling Luo | Jinchan Qu | Albert Steppi | Ramakanth Kavuluru | Tung Tran | S. Matos | Chen-Kai Wang | Rui Antunes | Zhuang Liu | B. Altinel | Aris Fergadis
[1] Sampo Pyysalo,et al. Overview of BioNLP Shared Task 2013 , 2013, BioNLP@ACL.
[2] Karin M. Verspoor,et al. BioC: a minimalist approach to interoperability for biomedical text processing , 2013, AMIA.
[3] K. Cohen,et al. Overview of BioCreative II gene normalization , 2008, Genome Biology.
[4] Zhiyong Lu,et al. GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains , 2015, BioMed research international.
[5] Yongqun He,et al. The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature , 2016, BioData Mining.
[6] Alfonso Valencia,et al. Overview of BioCreAtIvE: critical assessment of information extraction for biology , 2005, BMC Bioinformatics.
[7] F. Collins,et al. A new initiative on precision medicine. , 2015, The New England journal of medicine.
[8] Fred E. Cohen,et al. Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors , 2004, Bioinform..
[9] Raja Mazumder,et al. DiMeX: A Text Mining System for Mutation-Disease Association Extraction , 2016, PloS one.
[10] Yoon Kim,et al. Convolutional Neural Networks for Sentence Classification , 2014, EMNLP.
[11] W. John Wilbur,et al. BioC viewer: a web-based tool for displaying and merging annotations in BioC , 2016, Database J. Biol. Databases Curation.
[12] Paloma Martínez,et al. The DDI corpus: An annotated corpus with pharmacological substances and drug-drug interactions , 2013, J. Biomed. Informatics.
[13] Zhiyong Lu,et al. The CHEMDNER corpus of chemicals and drugs and its annotation principles , 2015, Journal of Cheminformatics.
[14] K. Bretonnel Cohen,et al. MutationFinder: a high-performance system for extracting point mutation mentions from text , 2007, Bioinform..
[15] Hongfei Lin,et al. Document triage for identifying protein–protein interactions affected by mutations: a neural network ensemble approach , 2018, Database J. Biol. Databases Curation.
[16] Jeyakumar Natarajan,et al. Overview of the interactive task in BioCreative V , 2015, Database J. Biol. Databases Curation.
[17] S. Perkins,et al. CoagMDB: a database analysis of missense mutations within four conserved domains in five vitamin K–dependent coagulation serine proteases using a text‐mining tool , 2008, Human mutation.
[18] Sampo Pyysalo,et al. Overview of BioNLP’09 Shared Task on Event Extraction , 2009, BioNLP@HLT-NAACL.
[19] Kara Dolinski,et al. The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions , 2017, Database J. Biol. Databases Curation.
[20] W. John Wilbur,et al. PIE the search: searching PubMed literature for protein interaction information , 2012, Bioinform..
[21] W. John Wilbur,et al. Assisting manual literature curation for protein–protein interactions using BioQRator , 2014, Database J. Biol. Databases Curation.
[22] Zhiyong Lu,et al. BioCreative V CDR task corpus: a resource for chemical disease relation extraction , 2016, Database J. Biol. Databases Curation.
[23] Zhiyong Lu,et al. tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine , 2018, Bioinform..
[24] Zhiyong Lu,et al. Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health. , 2016, Advances in experimental medicine and biology.
[25] Steven J. Simske,et al. On the Helmholtz Principle for Data Mining , 2012, 2012 Third International Conference on Emerging Security Technologies.
[26] Kara Dolinski,et al. The BioGRID interaction database: 2017 update , 2016, Nucleic Acids Res..
[27] Steven J. Simske,et al. Rapid change detection and text mining , 2011 .
[28] Diyi Yang,et al. Hierarchical Attention Networks for Document Classification , 2016, NAACL.
[29] Zhiyong Lu,et al. Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II , 2012, Database J. Biol. Databases Curation.
[30] Burkhard Rost,et al. nala: text mining natural language mutation mentions , 2017, Bioinform..
[31] Zhiyong Lu,et al. Beyond accuracy: creating interoperable and scalable text-mining web services , 2016, Bioinform..
[32] Zhiyong Lu,et al. SR4GN: A Species Recognition Software Tool for Gene Normalization , 2012, PloS one.
[33] R. Apweiler,et al. MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data , 2008, Genome Biology.
[34] Juliane Fluck,et al. Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL) , 2016, Database J. Biol. Databases Curation.
[35] Sutanu Chakraborti,et al. Sprinkling: Supervised Latent Semantic Indexing , 2006, ECIR.
[36] Arzucan Özgür,et al. Classification using Ontology and Semantic Values of Terms for Mining Protein Interactions and Mutations , 2017 .
[37] Miguel Pignatelli,et al. Database: The Journal of Biological Databases and Curation , 2016 .
[38] A. Valencia,et al. Overview of the protein-protein interaction annotation extraction task of BioCreative II , 2008, Genome Biology.
[39] Yifan Peng,et al. BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations , 2017, BioNLP.
[40] K. Bretonnel Cohen,et al. Text mining for the biocuration workflow , 2012, Database J. Biol. Databases Curation.
[41] André L. M. Santos,et al. BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID , 2016, Database J. Biol. Databases Curation.
[42] Petr Sojka,et al. Software Framework for Topic Modelling with Large Corpora , 2010 .
[43] Georgios Balikas,et al. An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition , 2015, BMC Bioinformatics.
[44] Kotagiri Ramamohanarao,et al. Exploiting graph kernels for high performance biomedical relation extraction , 2018, Journal of Biomedical Semantics.
[45] W. John Wilbur,et al. Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora , 2014, Database J. Biol. Databases Curation.
[46] Zhiyong Lu,et al. Overview of the BioCreative III Workshop , 2011, BMC Bioinformatics.
[47] Rafael C. Jimenez,et al. The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases , 2013, Nucleic Acids Res..
[48] Zhiyong Lu,et al. Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine , 2016, PLoS Comput. Biol..
[49] Zhiyong Lu,et al. BioCreative III interactive task: an overview , 2011, BMC Bioinformatics.
[50] Zhiyong Lu,et al. tmVar: a text mining approach for extracting sequence variants in biomedical literature , 2013, Bioinform..
[51] Zhiyong Lu,et al. The BioCreative VI Precision Medicine Track corpus Selection , annotation and curation of protein-protein interactions affected by mutations in scientific literature , 2017 .
[52] A. Valencia,et al. Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge , 2008, Genome Biology.
[53] Yifan Peng,et al. BioC interoperability track overview , 2014, Database J. Biol. Databases Curation.
[54] Jeyakumar Natarajan,et al. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task , 2013, Database J. Biol. Databases Curation.
[55] Zhiyong Lu,et al. On expert curation and scalability: UniProtKB/Swiss-Prot as a case study , 2017, Bioinform..
[56] Jian Su,et al. Supervised and Traditional Term Weighting Methods for Automatic Text Categorization , 2009, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[57] Yifan Peng,et al. Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task , 2016, Database J. Biol. Databases Curation.
[58] Trey Ideker,et al. Genotype to phenotype via network analysis. , 2013, Current opinion in genetics & development.
[59] Zhiyong Lu,et al. PubTator: a web-based text mining tool for assisting biocuration , 2013, Nucleic Acids Res..