Paper Info
Title
BioC viewer: a web-based tool for displaying and merging annotations in BioC.
Abstract
BioC is an XML-based format designed to provide interoperability for text mining tools and manual curation results. A challenge of BioC as a standard format is to align annotations from multiple systems. Ideally, this should not be a major problem if users follow guidelines given by BioC key files. Nevertheless, the misalignment between text and annotations happens quite often because different systems tend to use different software development environments, e.g. ASCII vs. Unicode. We first implemented the BioC Viewer to assist BioGRID curators as a part of the BioCreative V BioC track (Collaborative Biocurator Assistant Task). For the BioC track, the BioC Viewer helped curate protein-protein interaction and genetic interaction pairs appearing in full-text articles. Here, we describe the BioC Viewer itself as well as improvements made to the BioC Viewer since the BioCreative V Workshop to address the misalignment issue of BioC annotations. While uploading BioC files, a BioC merge process is offered when there are files from the same full-text article. If there is a mismatch between an annotated offset and text, the BioC Viewer adjusts the offset to correctly align with the text. The BioC Viewer has a user-friendly interface, where most operations can be performed within a few mouse clicks. The feedback from BioGRID curators has been positive for the web interface, particularly for its usability and learnability.
Year
DOI
Venue
2016
10.1093/database/baw106
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
Field
DocType
Volume
World Wide Web,Information retrieval,XML,Computer science,Interoperability,Usability,Biocurator,Data curation,ASCII,Web application,Unicode
Journal
2016
ISSN
Citations 
PageRank 
1758-0463
4
0.41
References 
Authors
11
4
Name
Order
Citations
PageRank
Soo-Yong Shin119617.20
Sun Kim2151.72
W. John Wilbur343045.66
Dongseop Kwon419316.67