BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID
| Author(s) | Kim,Sun | |
| Author(s) | Dogan,Rezarta Islamaj | |
| Author(s) | Chatr-Aryamontri,Andrew | |
| Author(s) | Chang,Christie S. | |
| Author(s) | Oughtred,Rose | |
| Author(s) | Rust,Jennifer | |
| Author(s) | Batista-Navarro,Riza | |
| Author(s) | Carter,Jacob | |
| Author(s) | Ananiadou,Sophia | |
| Author(s) | Matos,Sergio | |
| Author(s) | Santos,Andre | |
| Author(s) | Campos,David | |
| Author(s) | Oliveira,Jose Luis | |
| Author(s) | Singh,Onkar | |
| Author(s) | Jonnagaddala,Jitendra | |
| Author(s) | Dai,Hong-Jie | |
| Author(s) | Su,Emily Chia-Yu | |
| Author(s) | Chang,Yung-Chun | |
| Author(s) | Su,Yu-Chen | |
| Author(s) | Chu,Chun-Han | |
| Author(s) | Chen,Chien Chin | |
| Author(s) | Hsu,Wen-Lian | |
| Author(s) | Peng,Yifan | |
| Author(s) | Arighi,Cecilia | |
| Author(s) | Wu,Cathy H. | |
| Author(s) | Vijay-Shanker,K. | |
| Author(s) | Aydin,Ferhat | |
| Author(s) | Husunbeyi,Zehra Melce | |
| Author(s) | Ozgur,Arzucan | |
| Author(s) | Shin,Soo-Yong | |
| Author(s) | Kwon,Dongseop | |
| Author(s) | Dolinski,Kara | |
| Author(s) | Tyers,Mike | |
| Author(s) | Wilbur,W. John | |
| Author(s) | Comeau,Donald C. | |
| Ordered Author | Sun Kim, Rezarta Islamaj Do gan, Andrew Chatr-Aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Se� rgio Matos, Andre� Santos, David Campos, Jose�Lu?s Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen,Wen-Lian Hsu,Yifan Peng, Cecilia Arighi,Cathy H. Wu, K. Vijay-Shanker, Ferhat Ayd?n, Zehra Melce Husunbey, Arzucan Ozgu, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur and Donald C. Comeau | |
| UD Author | Arighi, Cecilia Noemi; Wu, Cathy Huey-Hwa; Shanker, Vijay K | |
| Date Accessioned | 2017-07-13T20:01:50Z | |
| Date Available | 2017-07-13T20:01:50Z | |
| Publication Date | 8/2/16 | |
| Description | Publisher's PDF | |
| Abstract | BioC is a simple XML format for text, annotations and relations, and was Developmenteloped to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant system for BioGRID curation. In this paper, we describe the framework of the collaborative BioC task and discuss our findings based on the user survey. This track consisted of eight subtasks including gene/protein/organism named entity recognition, protein-protein/genetic interaction passage identification and annotation visualization. Using BioC as their data-sharing and communication medium, nine teams, world-wide, participated and contributed either new methods or improvements of existing tools to address different subtasks of the BioC track. Results from different teams were shared in BioC and made available to other teams as they addressed different subtasks of the track. In the end, all submitted runs were merged using a machine learning classifier to produce an optimized output. The biocurator assistant system was evaluated by four BioGRID curators in terms of practical usability. The curators' feedback was overall positive and highlighted the user-friendly design and the convenient gene/protein curation tool based on text mining. | |
| Department | University of Delaware, Computer and Information Sciences University of Delaware, Center for Bioinformatics and Computational Biology | |
| Citation | Kim, S., Dogan, R. I., Chatr-Aryamontri, A., Chang, C. S., Oughtred, R., Rust, J., Comeau, D. C. (2016). BioCreative V BioC track overview: Collaborative biocurator assistant task for BioGRID. Database-the Journal of Biological Databases and Curation, , baw121. doi:10.1093/database/baw121 | |
| DOI | 10.1093/database/baw121 | |
| ISSN | 1758-0463 | |
| URL | http://udspace.udel.edu/handle/19716/21541 | |
| Language | English | |
| Publisher | Oxford University Press | |
| dc.rights | This work is written by US Government employees and is in the public domain in the US | |
| dc.source | Database-the Journal of Biological Databases and Curation | |
| dc.source.uri | https://academic.oup.com/database/article-lookup/doi/10.1093/database/baw121 | |
| Title | BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID | |
| Type | Article |
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