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BioC Viewer: a web-based tool for displaying and merging annotations in BioC#

Abstract

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 to curate protein-protein interaction and genetic interaction pairs appearing in full-text articles. 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. During the evaluation of the BioC Viewer, problems related to misaligned annotations were encountered. 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. 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.

Tested systems

  • Rails: 4.2.5.1
  • MySQL: 5.7.10
  • Ruby 2.2
  • OS: MacOS X 10.11 (development) and Ubuntu 14.04.3 LTS (production)

How to run

  1. You need to install git, ruby, rails, and MySQL first.
  2. Clone this repository: git clone https://github.com/dongseop/bioc_viewer.git
  3. cd bioc_viewer
  4. bundle install
  5. You need to create your own 'database.yml' and 'secrets.yml' in 'config' directory. You may refer sample files in the config directory.
  6. rake db:create
  7. rake db:migrate
  8. rails s

How to test

Sorry. Missing test codes.

Contributing

  1. Fork it
  2. Create your feature branch (git checkout -b my-new-feature)
  3. Commit your changes (git commit -am 'Add some feature')
  4. Push to the branch (git push origin my-new-feature)
  5. Create new Pull Request

LICENSE

Copyright © 2016, Dongseop Kwon

Released under the Apache License License 2.0

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Web interface for displaying and merging annotations in BioC

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