BioCreative Virtual Issue
This Database virtual issue is themed around BioCreative: Critical Assessment of Information Extraction in Biology, an international community-wide effort for evaluating text mining and information extraction systems applicable to the biological field. The aim is to drive the development of practically relevant text mining systems in order that these may facilitate information access to biologists and also provide tools that may be integrated into the biocuration workflow and the searching processes conducted by databases.
The following articles were subject to the journal’s normal peer review process, and are collected together here as a ‘virtual issue’.
Biocreative VI
Extracting chemical-protein relations with ensembles of SVM and deep learning models.
Yifan Peng, Anthony Rios, Ramakanth Kavuluru and Zhiyong Lu.
Database 2018: bay073 doi: 10.1093/database/bay073
Leveraging prior knowledge for protein-protein interaction extraction with memory network.
Huiwei Zhou, Zhuang Liu, Shixian Ning, Yunlong Yang, Chengkun Lang, Yingyu Lin and Kun Ma.
Database 2018: bay071 doi: 10.1093/database/bay071
Improving the learning of chemical-protein interactions from literature using transfer learning and specialized word embeddings.
P Corbett and J Boyle.
Database 2018: bay066 doi: 10.1093/database/bay066
Chemical-gene relation extraction using recursive neural network
Sangrak Lim and Jaewoo Kang
Database 2018: bay060 doi: 10.1093/database/bay060
SPRENO: a BioC module for identifying organism terms in figure captions.
Hong-Jie Dai and Onkar Singh
Database 2018: bay048 doi: 10.1093/database/bay048
Assisting document triage for human kinome curation via machine learning
Yi-Yu Hsu, Chih-Hsuan Wi and Zhiyong Lu
Database 2018: bay091 doi: 10.1093/database/bay091
An end-to-end deep learning architecture for extracting protein-protein interactions affected by genetic mutations
Tung Tran and Ramakanth Kavuluru
Database 2018: bay092 doi: 10.1093/database/bay092
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling
Suwisa Kaewphan, Kai Hakala, Niko Miekka, Tapio Salakoski and Filip Ginter
Database 2018: bay096 doi: 10.1093/database/bay096
Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach
Ling Luo, Zhihao Yang, Hongfei Lin and Juan Wang
Large-scale automated machine reading discovers new cancer-driving mechanisms
Marco A Valenzuela-Escárcega, Özgün Babur, Gus Hahn-Powell, Dane Bell, Thomas Hicks, Enrique Noriega-Atala, Xia Wang, Mihai Surdeanu, Emek Demir and Clayton T Morrison
Database 2018: bay098 doi:10.1093/database/bay098
Extracting chemical-protein relations using attention-based neural networks
Sijia Liu, Feichen Shen, Ravikumar Komandur Elayavilli, Yanshan Wang, Majid Rastegar-Majarad, Vipin Chaudhary and Hongfang Liu
Database 2018: bay102 doi: 10.1093/database/bay102
Overview of the BioCreative VI text-mining services for Kinome Curation Track
Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahnda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu and Patrick Ruch
Database 2018: bay104 doi: 10.1093/database/bay104
LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task
Neha Warikoo, Yung-Chun Chang and Wen-Lian Hsu
Database 2018: bay108 doi: 10.1093/database/bay108
Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction
Farrokh Mehryary, Jari Björne, Tapio Salakoski, and Filip Ginter
Database 2018: bay120 doi: 10.1093/database/bay120
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics
Qingyu Chen, Nagesh C Panyam, Aparna Elangovan and Karin Verspoor
Database: 2018: bay122 doi: 10.1093/database/bay122
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature
Jia Ren, Gang Li, Karen Ross, Cecilia Arighi, Peter McGarvel , Shruti Rao, Julie Cowart, Subha Madhavan, K Vijay-Shanker and Cathy H Wu
Database 2018: bay128 doi: 10.1093/database/bay128
Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering
Pei-Yau Lung, Zhe He, Tingting Zhao, Disa Yu and Jinfeng Zhang
Database 2019: bay138 doi: 10.1093/database/bay138
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine
Rezarta Islamaj Do?an, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Alt?nel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, and Zhiyong Lu
Database 2019: bay147 doi: 10.1093/database/bay147
BioCreative V
Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis
Yalbi Itzel Balderas-Martínez, Fabio Rinaldi, Gabriela Contreras, Hilda Solano-Lira, Mishael Sánchez-Pérez, Julio Collado-Vides, Moisés Selman and Annie Pardo
Database 2017: bax030 doi:10.1093/database/bax030
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation
Evangelos Pafilis, Pier Luigi Buttigieg, Barbra Ferrell, Emiliano Pereira, Julia Schnetzer, Christos Arvanitidis and Lars Juhl Jensen
Database 2016: baw005 doi:10.1093/database/baw005
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers and Zhiyong Lu
Database Vol. 2016, baw032 doi:10.1093/database/baw032
CD-REST: a system for extracting chemical-induced disease relation in literature
Jun Xu, Yonghui Wu, Yaoyun Zhang, Jingqi Wang, Hee-Jin Lee and Hua Xu
Database Vol. 2016, baw036 doi:10.1093/database/baw036
Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall
Daniel M. Lowe, Noel M. O’Boyle and Roger A. Sayle
Database Vol. 2016, baw039 doi:10.1093/database/baw039
Chemical-induced disease relation extraction with various linguistic features
Jinghang Gu, Longhua Qian and Guodong Zhou
Database Vol. 2016, baw042 doi:10.1093/database/baw042
Extraction of chemical-induced diseases using prior knowledge and textual information
Ewoud Pons, Benedikt F.H. Becker, Saber A. Akhondi, Zubair Afzal, Erik M. van Mulligen and Jan A. Kors
Database Vol. 2016, baw046 doi:10.1093/database/baw046
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning
Yaoyun Zhang, Jun Xu, Hui Chen, Jingqi Wang, Yonghui Wu, Manu Prakasam and Hua Xu
Database Vol. 2016, baw049 doi:10.1093/database/baw049
Exploiting syntactic and semantics information for chemical–disease relation extraction
Huiwei Zhou, Huijie Deng, Long Chen, Yunlong Yang, Chen Jia and Degen Huang
Database Vol. 2016, baw048 doi:10.1093/database/baw048
A crowdsourcing workflow for extracting chemical-induced disease relations from free text
Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good and Andrew I. Su
Database Vol. 2016, baw051 doi:10.1093/database/baw051
Chemical entity recognition in patents by combining dictionary-based and statistical approaches
Saber A. Akhondi, Ewoud Pons, Zubair Afzal, Herman van Haagen, Benedikt F.H. Becker, Kristina M. Hettne, Erik M. van Mulligen and Jan A. Kors
Database Vol. 2016, baw061 doi:10.1093/database/baw061
BioCreative V CDR task corpus: a resource for chemical disease relation extraction
Jiao Li, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers and Zhiyong Lu
Database Vol. 2016, baw068 doi:10.1093/database/baw068
BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text
Po-Ting Lai, Yu-Yan Lo, Ming-Siang Huang, Yu-Cheng Hsiao, and Richard Tzong-Han Tsai
Database Vol. 2016, baw064 doi:10.1093/database/baw064
BioC-compatible full-text passage detection for protein–protein interactions using extended dependency graph
Yifan Peng, Cecilia Arighi, Cathy H. Wu, and K. Vijay-Shankeri
Database Vol. 2016, baw072 doi:10.1093/database/baw072
Chemical entity recognition in patents by combining dictionary-based and statistical approaches
Saber A. Akhondi, Ewoud Pons, Zubair Afzal, Herman van Haagen, Benedikt F.H. Becker, Kristina M. Hettne, Erik M. van Mulligen, and Jan A. Kors
Database Vol. 2016, baw061 doi:10.1093/database/baw061
BELTracker: evidence sentence retrieval for BEL statements
Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, and Hongfang Liu
Database Vol. 2016, baw079 doi:10.1093/database/baw079
Argo: enabling the development of bespoke workflows and services for disease annotation
Riza Batista-Navarro, Jacob Carter, and Sophia Ananiadou
Database Vol. 2016, baw066 doi:10.1093/database/baw066
Mining chemical patents with an ensemble of open systems
Robert Leaman, Chih-Hsuan Wei, Cherry Zou, and Zhiyong Lu
Database Vol. 2016, baw065 doi:10.1093/database/baw065
A knowledge-poor approach to chemical-disease relation extraction
Firoj Alam, Anna Corazza, Alberto Lavelli, and Roberto Zanoli
Database Vol. 2016, baw071 doi:10.1093/database/baw071
MET network in PubMed: a text-mined network visualization and curation system
Hong-Jie Dai, Chu-Hsien Su, Po-Ting Lai, Ming-Siang Huang, Jitendra Jonnagaddala, Toni Rose Jue, Shruti Rao, Hui-Jou Chou, Marija Milacic, Onkar Singh, Shabbir Syed-Abdul, and Wen-Lian Hsu
Database Vol. 2016, baw090 doi:10.1093/database/baw090
HITSZ_CDR: an end-to-end chemical and disease relation extraction system for BioCreative V
Haodi Li, Buzhou Tang, Qingcai Chen, Kai Chen, Xiaolong Wang, Baohua Wang, and Zhe Wang
Database Vol. 2016, baw077 doi:10.1093/database/baw077
AuDis: an automatic CRF-enhanced disease normalization in biomedical text
Hsin-Chun Lee, Yi-Yu Hsu, and Hung-Yu Kao
Database Vol. 2016, baw091 doi:10.1093/database/baw091
Mining clinical attributes of genomic variants through assisted literature curation in Egas
Sérgio Matos, David Campos, Renato Pinho, Raquel M. Silva, Matthew Mort, David N. Cooper, and José Luís Oliveira
Database Vol. 2016, baw096 doi:10.1093/database/baw096
PIPE: A Protein-protein Interaction Passage Extraction Module for BioCreative Challenge
Yung-Chun Chang, Chun-Han Chu, Yu-Chen Su, Chien Chin Chen, and Wen-Lian Hsu
Database Vol. 2016, baw101 doi: 10.1093/database/baw101
Sieve-based coreference resolution enhances semi-supervised learning model for chemical-induced disease relation extraction
Hoang-Qing Le, Mai-Vu Tran, Thanh Hai Dang, Quang-Thuy Ha, and Nigel Collier
Database Vol. 2016, baw102 doi: 10.1093/database/baw102
BioC Viewer: a web-based tool for displaying and merging annotations in BioC
Soo-Yong Shin, Sun Kim, John Wilbur, and Dongseop Kwon
Database Vol. 2016, baw106 doi: 10.1093/database/baw106
Crowdsourcing and curation: perspectives from biology and natural language processing
Lynette Hirschman, Karën Fort, Stephanie Boue, Nikos Kyrpides, Rezarta Islamaj Dogan, and Kevin Cohen
Database Vol. 2016, baw119 doi: 10.1093/database/baw115
Overview of the Interactive Task in BioCreative V
Qinghua Wang, Shabbir Syed-Abdul, Lara Almeida, Sophia Ananiadou, Yalbi Balderas-Martinez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios Gkoutos, Afroza Irin, Lars Jensen, Silvia Jimenez, Toni Rose Jue, Ingrid Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Subramani Suresh, Hamsa Tadepally, Loukia Tsaprouni, Nicole Vasilevsky, Xiaodong Wang, Andrew Chatr-Aryamontri, Stanley Laulederkind, Sherri Matis-Mitchell, Jo McEntyre, Sandra Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary Schaeffer, Cathy Wu, Lynette Hirschman, and Cecilia Arighi
Database Vol. 2016, baw119 doi: 10.1093/database/baw119
BioCreative V BioC Track Overview: Collaborative Biocurator Assistant Task for BioGRID
Sun Kim, Rezarta Islamaj Dogan, Andrew Chatr-Aryamontri, Christie Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chan Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydin, Zebra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, John Wilbur, and Donald Comeau
Database Vol. 2016, baw121 doi: 10.1093/database/baw121
The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge
Martín Pérez-Pérez, Gael Pérez-Rodríguez, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, and Anália Lourenço
Database Vol. 2016, baw120 doi: 10.1093/database/baw120
NERChem: Adapting NERBio to Chemical Patents via Full-token Features and Named Entity Feature with Chemical Sub-Class Composition
Tzong-Han Tsai, Yu Hsiao, and Po-Ting Lai
Database Vol. 2016, baw135 doi: 10.1093/database/baw135
The BEL Information Extraction Workflow (BELIEF): Evaluation in the BioCreative V BEL and IAT track
Sumit Madan, Sven Hodapp, Philipp Senger, Sam Ansari, Justyna Szostak, Julia Hoeng, Manuel Peitsch, and Juliane Fluck
Database Vol. 2016, baw136 doi: 10.1093/database/baw136
Disease Named Entity Recognition by Combining Conditional Random Fields and Bidirectional Recurrent Neural Networks
Qikang Wei, Tao Chen, Ruifeng Xu, Yulan He, and Lin Gui
Database Vol. 2016, baw140 doi: 10.1093/database/baw140
The BioC-BioGRID corpus: Full text articles annotated for curation of protein-protein and genetic interactions
Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-Aryamontri, Christie Chang, Rose Oughtred, Jennifer Rust, John Wilbur, Donald Comeau, Kara Dolinski, and Mike Tyers
Database Vol. 2016, baw147 doi: 10.1093/database/baw147
BELXtractor: Adapting a rule-based relation extraction system to extract Biological Expression Language (BEL) statements from Bio-Medical Literature Evidence Sentences
Ravikumar Komandurelayavilli, Majid Rastegar-Mojarad, and Hongfang Liu
Database Vol. 2016, baw156 doi: 10.1093/database/baw156
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges
Ayush Singhal, Robert Leaman, Natalie Calett, Thomas Lemberger, Jo McEntyre, Shawn Polson, Ioannis Xenarios, Cecilia Arighi, and Zhiyong Lu
Database Vol. 2016, baw161 doi: 10.1093/database/baw161
Automatic Query Generation using Word Embeddings for Retrieving Passages Describing Experimental Methods
Arzucan Özgür, Ferhat Aydin, and Zebra M. Hünsünbeyi
Database Vol. 2016, baw166 doi: 10.1093/database/baw166
Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text
Àlex Bravo, Tong Shu Li, Andrew I. Su, Benjamin M. Good, and Laura I. Furlong
Database Vol. 2016, baw094 doi: 10.1093/database/baw094
Coreference resolution improves extraction of Biological Expression Language statements from texts
Miji Choi, Haibin Liu, William Baumgartner, Justin Zobel, and Karin Verspoor
Database Vol. 2016, baw076 doi: 10.1093/database/baw076
NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions
Hong-Jie Dai, Onkar Singh, Jitendra Jonnagaddala, and Emily Chia-Yu Su
Database Vol. 2016, baw111 doi: 10.1093/database/baw111
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL)
Juliane Fluck, Sumit Madan, Sam Ansari, Alpha T. Kodamullil, Reagon Karki, Majid Rastegar-Mojarad, Natalie L. Catlett, William Hayes, Justyna Szostak, Julia Hoeng, and Manuel Peitsch
Database Vol. 2016, baw113 doi: 10.1093/database/baw113
BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language
Fabio Rinaldi, Tilia Renate Ellendorff, Sumit Madan, Simon Clematide, Adrian van der Lek, Theo Mevissen, and Juliane Fluck
Database Vol. 2016, baw067 doi: 10.1093/database/baw067
In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis
Matheus Eloy Franco, Tamires Aparecida Bitencourt, Mozart Marins, and Ana Lúcia Fachin
Database Vol. 2017, bax035 doi: 10.1093/database/bax035
BioCreative IV
EDITORIAL: BioCreative-IV virtual issue
Cecilia N. Arighi, Cathy H. Wu, Kevin B. Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, John W. Wilbur, and Thomas C. Wiegers
Database 2014: bau039 doi:10.1093/database/bau039
A robust data-driven approach for gene ontology annotation
Yanpeng Li and Hong Yu
Database 2014: bau113 doi:10.1093/database/bau113
Unsupervised gene function extraction using semantic vectors
Ehsan Emadzadeh, Azadeh Nikfarjam, Rachel E. Ginn, and Graciela Gonzalez
Database 2014: bau084 doi:10.1093/database/bau084
Integrating information retrieval with distant supervision for Gene Ontology annotation
Dongqing Zhu, Dingcheng Li, Ben Carterette, and Hongfang Liu
Database 2014: bau087 doi:10.1093/database/bau087
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information
Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, and Cathy H. Wu
Database 2014: bau081 doi:10.1093/database/bau081
Overview of the gene ontology task at BioCreative IV
Yuqing Mao, Kimberly Van Auken, Donghui Li, Cecilia N. Arighi, Peter McQuilton, G. Thomas Hayman, Susan Tweedie, Mary L. Schaeffer, Stanley J. F. Laulederkind, Shur-Jen Wang, Julien Gobeill, Patrick Ruch, Anh Tuan Luu, Jung-jae Kim, Jung-Hsien Chiang, Yu-De Chen, Chia-Jung Yang, Hongfang Liu, Dongqing Zhu, Yanpeng Li, Hong Yu, Ehsan Emadzadeh, Graciela Gonzalez, Jian-Ming Chen, Hong-Jie Dai, and Zhiyong Lu
Database 2014: bau086 doi:10.1093/database/bau086
Closing the loop: from paper to protein annotation using supervised Gene Ontology classification
Julien Gobeill, Emilie Pasche, Dina Vishnyakova, and Patrick Ruch
Database 2014: bau088 doi:10.1093/database/bau088
LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations
Hong-Jie Dai, Johnny Chi-Yang Wu, Wei-San Lin, Aaron James F. Reyes, Mira Anne C. dela Rosa, Shabbir Syed-Abdul, Richard Tzong-Han Tsai, and Wen-Lian Hsu
Database 2014: bau085 doi:10.1093/database/bau085
tmBioC: improving interoperability of text-mining tools with BioC
Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, and Zhiyong Lu
Database 2014: bau073 doi:10.1093/database/bau073
BC4GO: a full-text corpus for the BioCreative IV GO task
Kimberly Van Auken, Mary L. Schaeffer, Peter McQuilton, Stanley J. F. Laulederkind, Donghui Li, Shur-Jen Wang, G. Thomas Hayman, Susan Tweedie, Cecilia N. Arighi, James Done, Hans-Michael Müller, Paul W. Sternberg, Yuqing Mao, Chih-Hsuan Wei, and Zhiyong Lu
Database 2014: bau074 doi:10.1093/database/bau074
Assisting manual literature curation for protein–protein interactions using BioQRator
Dongseop Kwon, Sun Kim, Soo-Yong Shin, Andrew Chatr-aryamontri, and W. John Wilbur
Database 2014: bau067 doi:10.1093/database/bau067
Web services-based text-mining demonstrates broad impacts for interoperability and process simplification
Thomas C. Wiegers, Allan Peter Davis, and Carolyn J. Mattingly
Database 2014: bau050 doi:10.1093/database/bau050
BioC interoperability track overview
Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Do?an, Antonio Jimeno Yepes, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J. Mattingly, Mariana Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, and W. John Wilbur
Database 2014: bau053 doi:10.1093/database/bau053
Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12
Socorro Gama-Castro, Fabio Rinaldi, Alejandra López-Fuentes, Yalbi Itzel Balderas-Martínez, Simon Clematide, Tilia Renate Ellendorff, Alberto Santos-Zavaleta, Hernani Marques-Madeira, and Julio Collado-Vides
Database 2014: bau049 doi:10.1093/database/bau049
Processing biological literature with customizable Web services supporting interoperable formats
Rafal Rak, Riza Theresa Batista-Navarro, Jacob Carter, Andrew Rowley, and Sophia Ananiadou
Database 2014: bau064 doi:10.1093/database/bau064
Text-mining-assisted biocuration workflows in Argo
Rafal Rak, Riza Theresa Batista-Navarro, Andrew Rowley, Jacob Carter, and Sophia Ananiadou
Database 2014: bau070 doi:10.1093/database/bau070
BioC implementations in Go, Perl, Python and Ruby
Wanli Liu, Rezarta Islamaj Do?an, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, and Donald C. Comeau
Database 2014: bau059 doi:10.1093/database/bau059
Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus
Donald C. Comeau, Haibin Liu, Rezarta Islamaj Do?an, and W. John Wilbur
Database 2014: bau056 doi:10.1093/database/bau056
Egas: a collaborative and interactive document curation platform
David Campos, Jóni Lourenço, Sérgio Matos, and José Luís Oliveira
Database 2014: bau048 doi:10.1093/database/bau048
Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora
Rezarta Islamaj Do?an, Donald C. Comeau, Lana Yeganova, and W. John Wilbur
Database 2014: bau044 doi:10.1093/database/bau044
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles
Juan Miguel Cejuela, Peter McQuilton, Laura Ponting, Steven J. Marygold, Raymund Stefancsik, Gillian H. Millburn, Burkhard Rost, the FlyBase Consortium
Database 2014 : bau033 doi: 10.1093/database/bau033
iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system
Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu and K. Vijay-Shanker
Database 2014 : bau038 doi: 10.1093/database/bau038
BioC: a minimalist approach to interoperability for biomedical text processing
Donald C. Comeau, Rezarta Islamaj Do?an, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, and W. John Wilbur
Database 2013: bat064 doi:10.1093/database/bat064
BioCreative III
Editorial
BioCreative - 2012 Virtual Issue
Cathy H. Wu, Cecilia N. Arighi, Kevin B. Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Carolyn Mattingly, Alfonso Valencia, Thomas C. Wiegers, and W. John Wilbur
Database Vol. 2012, bas049; doi:10.1093/database/bas049
Track 1
Collaborative biocuration—text-mining development task for document prioritization for curation
Thomas C. Wiegers, Allan Peter Davis, and Carolyn J. Mattingly
Database Vol. 2012, bas037; doi:10.1093/database/bas037
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information
Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, and W. John Wilbur
Database Vol. 2012, bas042; doi:10.1093/database/bas042
Using the OntoGene pipeline for the triage task of BioCreative 2012
Fabio Rinaldi, Simon Clematide, Simon Hafner, Gerold Schneider, Gintarė Grigonytė, Martin Romacker, and Therese Vachon
Database Vol. 2013, bas053; doi:10.1093/database/bas053
Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database
Dina Vishnyakova, Emilie Pasche, and Patrick Ruch
Database Vol. 2012, bas050; doi:10.1093/database/bas050
Track 2
Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II
Zhiyong Lu and Lynette Hirschman
Database Vol. 2012, bas043; doi:10.1093/database/bas043
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR
Kimberly Van Auken, Petra Fey, Tanya Z. Berardini, Robert Dodson, Laurel Cooper, Donghui Li, Juancarlos Chan, Yuling Li, Siddhartha Basu, Hans-Michael Muller, Rex Chisholm, Eva Huala, Paul W. Sternberg and the WormBase Consortium
Database Vol. 2012, bas040; doi:10.1093/database/bas040
Building an efficient curation workflow for the Arabidopsis literature corpus
Donghui Li, Tanya Z. Berardini, Robert J. Muller, and Eva Huala
Database Vol. 2012, bas047; doi:10.1093/database/bas047
Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database
Harold J. Drabkin, Judith A. Blake, for the Mouse Genome Informatics Database
Database Vol. 2012, bas045; doi:10.1093/database/bas045
The Xenbase literature curation process
Jeff B. Bowes, Kevin A. Snyder, Christina James-Zorn, Virgilio G. Ponferrada, Chris J. Jarabek, Kevin A. Burns, Bishnu Bhattacharyya, Aaron M. Zorn, and Peter D. Vize
Database Vol. 2013, bas046; doi:10.1093/database/bas046
Opportunities for text mining in the FlyBase genetic literature curation workflow
Peter McQuilton and the FlyBase Consortium
Database Vol. 2012, bas039; doi:10.1093/database/bas039
Developing a biocuration workflow for AgBase, a non-model organism database
Lakshmi Pillai, Philippe Chouvarine, Catalina O. Tudor, Carl J. Schmidt, K. Vijay-Shanker, and Fiona M. McCarthy
Database Vol. 2012, bas038; doi:10.1093/database/bas038
Track 3
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task
Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila Dahdul, Paula Mabee, Donghui Li, Bethany Harris, Marc Gillespie, Silvia Jimenez, Phoebe Roberts, Lisa Matthews, Kevin Becker, Harold Drabkin, Susan Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Muller, Hong Cui, James P. Balhoff, Johnny Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, and Cathy Wu
Database Vol. 2013, bas056; doi:10.1093/database/bas056
PPInterFinder — a mining tool for extracting causal relations on human proteins from literature
Kalpana Raja, Suresh Subramani, and Jeyakumar Natarajan
Database Vol. 2013, bas052; doi:10.1093/database/bas052
The eFIP system for text mining of protein interaction networks of phosphorylated proteins
Catalina O. Tudor, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, and K. Vijay-Shanker
Database Vol. 2012, bas044; doi:10.1093/database/bas044
T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes
Hong-Jie Dai, Johnny Chi-Yang Wu, Richard Tzong-Han Tsai, Wen-Harn Pan, and Wen-Lian Hsu
Database Vol. 2013, bas061; doi:10.1093/database/bas061
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts
Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, and Zhiyong Lu
Database Vol. 2012, bas041; doi:10.1093/database/bas041
