Open Access Publications

Permanent URI for this collection

https://udspace.udel.edu/handle/19716/32580
Open access publications by faculty, staff, postdocs, and graduate students at the Center for Bioinformatics and Computational Biology.

Browse

Browsing Open Access Publications by Author "Ananiadou,Sophia"

Now showing 1 - 1 of 1
  • Thumbnail Image
    Item
    BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID
    (Oxford University Press, 8/2/16) Kim,Sun; Dogan,Rezarta Islamaj; Chatr-Aryamontri,Andrew; Chang,Christie S.; Oughtred,Rose; Rust,Jennifer; Batista-Navarro,Riza; Carter,Jacob; Ananiadou,Sophia; Matos,Sergio; Santos,Andre; Campos,David; Oliveira,Jose Luis; Singh,Onkar; Jonnagaddala,Jitendra; Dai,Hong-Jie; Su,Emily Chia-Yu; Chang,Yung-Chun; Su,Yu-Chen; Chu,Chun-Han; Chen,Chien Chin; Hsu,Wen-Lian; Peng,Yifan; Arighi,Cecilia; Wu,Cathy H.; Vijay-Shanker,K.; Aydin,Ferhat; Husunbeyi,Zehra Melce; Ozgur,Arzucan; Shin,Soo-Yong; Kwon,Dongseop; Dolinski,Kara; Tyers,Mike; Wilbur,W. John; Comeau,Donald C.; 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; Arighi, Cecilia Noemi; Wu, Cathy Huey-Hwa; Shanker, Vijay K
    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.
Copyright: Please look at individual material in order to see what the copyright and licensing terms are. Some material may be available for reuse under a Creative Commons license; other material may be the copyright of the individual author(s) or the publisher of the journal. Copyright lines may not be present in Accepted Manuscript versions so please refer to individual journal policies and/or look up the journal policies in Sherpa Romeo.