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.Database URL: http://viewer.bioqrator.org
Highlights
As text mining has gained popularity in the biomedical domain, many biomedical natural language processing tools have been developed and released to the public
We developed the BioC Viewer, a web interactive tool for visualizing and curating protein–protein interaction (PPI) and genetic interaction (GI) information [14]
The difference is in the ‘BioGRID’ mode the PPI/GI curation tool is visible and can be used for PPI/GI curation for BioGRID
Summary
As text mining has gained popularity in the biomedical domain, many biomedical natural language processing tools have been developed and released to the public. While many of these tools are useful, the difficulty comes from the integration with a user’s existing framework. This is due to the fact that relatively few tools support a common format that can be used for exchanging data. There are a number of text mining and curation tools [4,5,6,7,8] that support BioC
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