The entire proceedings (volume 1) are available here.
Table of Contents
-
Track 1 (BioC: Interoperability)
- PyBioC: a python implementation of the BioC core. Hernani Marques and Fabio Rinaldi. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 2-4
- Enhancing the Interoperability of iSimp by Using the BioC Format. Yifan Peng, Catalina O Tudor, Manabu Torii, Cathy H Wu and K Vijay-Shanker. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 5-9
- Improving Interoperability of Text Mining Tools with BioC. Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman and Zhiyong Lu. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 10-22
- Finding Abbreviations in Biomedical Literature: Three BioC-Compatible Modules and Three BioC-formatted Corpora. Rezarta Islamaj Doğan, Donald C. Comeau, Lana Yeganova and W. John Wilbur. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 23-30
- Extending BioC Implementation to More Languages. Wanli Liu, Donald C. Comeau, Rezarta Islamaj Doğan and W. John Wilbur. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 31-37
- 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. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 38-45
- Brat2BioC: conversion tool between brat and BioC. Antonio Jimeno Yepes, Mariana Neves and Karin Verspoor. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 46-53
- A Biomedical Semantic Role Labeling BioC Module for BioCreative IV. Po-Ting, Lai, Hong-Jie Dai, Johnny Chi-Yang Wu and Richard Tzong-Han Tsai. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 54-60
- NaCTeM’s BioC Modules and Resources for BioCreative IV. Rafal Rak, Riza Batista-Navarro, Andrew Rowley, Makoto Miwa, Jacob Carter and Sophia Ananiadou. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 61-67
- Web services-based text mining demonstrates broad impacts for interoperability and process simplification. Thomas C. Wiegers, Allan Peter Davis and Carolyn J. Mattingly. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 69-84
- NaCTeM CTD Web Services. Riza Batista-Navarro, Rafal Rak and Sophia Ananiadou. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 85-89
- OntoGene: CTD entity and action term recognition. Fabio Rinaldi, Simon Clematide, Tilia Renate Ellendorff and Hernani Marques. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 90-94
- Performance of a multi-class biomedical tagger on the BioCreative IV CTD task. S. V. Ramanan and P. Senthil Nathan. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 95-98
- A Web Service Annotation Framework for CTD Using the UIMA Concept Mapper. Andrew MacKinlay and Karin Verspoor. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 99-102
- Multi-stage Gene Mention Identification Method for BioCreative IV Track 3. Po-Ting, Lai, Kuan-Chieh, Chung, Johnny Chi-Yang Wu, Hong-Jie Dai and Richard Tzong-Han Tsai. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 103-107
- ToxiCat: Hybrid Named Entity Recognition services to support curation of the Comparative Toxicogenomic Database. Dina Vishnyakova, Julien Gobeill, Emilie Pasche and Patrick Ruch. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 108-113
- Adapting the OCMiner text processing system to the CTD controlled vocabulary. Matthias Irmer, Claudia Bobach, Timo Böhme, Ulf Laube, Anett Püschel and Lutz Weber. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 114-117
- The Gene Ontology Task at BioCreative IV. Yuqing Mao, Kimberly Van Auken, Donghui Li, Cecilia N. Arighi and Zhiyong Lu. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 119-127
- TCorpus Construction 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. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 128-138
- BiTeM/SIBtex group proceedings for BioCreative IV, Track 4: Gene Ontology curation. Gobeill Julien, Pasche Emilie, Vishnyakova Dina and Ruch Patrick. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 139-145
- Integrating Information Retrieval with Distant Supervision for Gene Ontology Annotation. Dongqing Zhu, Dingcheng Li, Ben Carterette and Hongfang Liu. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 146-155
- Unsupervised Information Extraction for Finding Gene Functions. Ehsan Emadzadeh, Azadeh Nikfarjam, Rachel E. Ginn and Dr. Graciela Gonzalez. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 156-161
- A Robust Data-Driven Approach for BioCreative IV GO Annotation Task. Yanpeng Li, Abhyuday Jagannat and Hong Yu. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 162-168
- Gene Ontology Evidence Sentence Retrieval Using Combinatorial Applications of Semantic Class and Rule Patterns. Jian-Ming Chen, Yung-Chun Chang, Johnny Chi-Yang Wu, Po-Ting Lai and Hong-Jie Dai. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 169-173
- Gene Ontology Concept Recognition using Cross-Products and Statistical Methods. Luu Anh Tuan, Jung-jae Kim, See-Kiong Ng. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 174-181
- Gene Ontology Evidence Sentence Extraction and Concept Extraction: Two Rule-Based Approaches. Yu-De Chen, Chia-Jung Yang, Wen-Gan Li, Chin-Yu Huang, Jung-Hsien Chiang. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 182-188
- BioCreative IV Interactive Task. Sherri Matis-Mitchell, Phoebe Roberts, Catalina O. Tudor and Cecilia N. Arighi. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 190-203
- Evaluation of the CellFinder pipeline in the BioCreative IV User Interactive task. Mariana Neves, Julian Braun, Alexander Diehl, G. Thomas Hayman, Shur-Jen Wang, Ulf Leser and Andreas Kurtz. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 204-213
- Assisted curation of growth conditions that affect gene expression in E. coli K-12. Socorro Gama-Castro, Fabio Rinaldi, Alejandra López-Fuentes, Yalbi Itzel Balderas-Martínez,
Simon Clematide, Tilia Renate Ellendorff and Julio Collado-Vides. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 214-218
- ODIN: a customizable literature curation tool. Fabio Rinaldi, Allan Peter Davis, Christopher Southan, Simon Clematide, Tilia Renate Ellendorff and Gerold Schneider. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 219-223
- MarkerRIF: An Interactive Curation System for Biomarker. Hong-Jie Dai, Chi-Yang Wu, Wei-San Lin, Richard Tzong-Han Tsai and Wen-Lian Hsu. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 224-233
- Supporting Document Triage with the SciKnowMine System in the Mouse Genome Informatics (MGI) Curation Process. Gully APC Burns, Marcelo Tallis, Hiroaki Onda, Kevin Cohen, James Kadin and Judith Blake. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 234-240
- BioQRator: a web-based interactive biomedical literature curating system. Dongseop Kwon, Sun Kim, Soo-Yong Shin and W. John Wilbur. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 241-246
- RLIMS-P: Literature-based curation of protein phosphorylation information. Manabu Torii, Gang Li, Zhiwen Li, Irem Çelen, Francesca Diella, Rose Oughtred, Cecilia Arighi,
Hongzhan Huang, K. Vijay-Shanker and Cathy H. Wu. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 247-253
- Egas – Collaborative Biomedical Annotation as a Service. David Campos , Joni Lourenço, Tiago Nunes, Rui Vitorino, Pedro Domingues, Sérgio Matos and
José Luís Oliveira. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 254-259
- tagtog: Interactive Human and Machine 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 and the FlyBase Consortium. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 260-269
- Customisable Curation Workflows in Argo. Rafal Rak, Riza Batista-Navarro, Andrew Rowley, Jacob Carter and Sophia Ananiadou. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 1, 270-278
Track 3 (CTD)
Track 4 (GO)
Track 5 (IAT)
