Skip Navigation

BioCreative Virtual Issue

BioCreative 2014


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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

BioC interoperability track overview
Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Doğan, 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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

BioC implementations in Go, Perl, Python and Ruby
Wanli Liu, Rezarta Islamaj Doğan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, and Donald C. Comeau
Database 2014: bau059 doi:10.1093/database/bau059
FREE Full Text

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus
Donald C. Comeau, Haibin Liu, Rezarta Islamaj Doğan, and W. John Wilbur
Database 2014: bau056 doi:10.1093/database/bau056
FREE Full Text

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
FREE Full Text

Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora
Rezarta Islamaj Doğan, Donald C. Comeau, Lana Yeganova, and W. John Wilbur
Database 2014: bau044 doi:10.1093/database/bau044
FREE Full Text

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
FREE Full Text

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
FREE Full Text

BioC: a minimalist approach to interoperability for biomedical text processing
Donald C. Comeau, Rezarta Islamaj Doğan, 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
FREE Full Text

BioCreative 2012


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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text

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
FREE Full Text